biological assessment for threatened, endangered, proposed,...

of 63

Biological Assessment

For

Threatened, Endangered, Proposed, and Sensitive Species

That May be Affected by the

O’Neil Creek Pond Project Happy Camp-Oak Knoll Ranger District

Klamath National Forest

Prepared and finalized by: Briam ThomasBriam ThomasBriam ThomasBriam Thomas Date: January 9, 2012

Brian Thomas, Fisheries Biologist, Supervisor’s Office

Approved by: Ken Harris Date: January 10, 2012

Ken Harris, Happy Camp-Oak Knoll District Ranger

of 63

PROJECT NAME: O’Neil Creek Pond Project

ADMINISTRATIVE UNIT: Klamath National Forest, Happy Camp-Oak Knoll Ranger

District

FOURTH FIELD WATERSHED: Klamath River

FIFTH FIELD WATERSHEDS: Seiad Creek-Klamath River

SEVENTH FIELD WATERSHEDS: O’Neil Creek

WATERSHED ANALYSES: Thompson/Seiad/Grider Ecosystem Analysis (1999)

NEPA DOCUMENTATION: Categorical Exclusion (documentation in progress)

ESA SPECIES CONSIDERED: Coho Salmon

ESA CRITICAL HABITAT CONSIDERED: Southern Oregon/Northern California Coast

coho salmon Critical Habitat (CH)

ESA DETERMINATIONS: May Affect Not Likely To Adversely Affect Southern

Oregon/Northern California Coast coho salmon ESU’s or their designated Critical Habitat.

SENSITIVE SPECIES CONSIDERED: 1) Upper Klamath-Trinity Rivers Chinook salmon (Chinook salmon)

2) Klamath Mountains Province steelhead trout (steelhead trout)

SENSITIVE SPECIES DETERMINATIONS: The O’Neil Creek Pond Project will have no

affect on loss of viability of steelhead trout or Chinook salmon in the short or long term, and will

have beneficial effects to habitat conditions in the long term through increase in quality and

quantity of rearing habitat for juvenile anadromous salmonids.

ESSENTIAL FISH HABITAT (EFH): The O’Neil Creek Pond Project may adversely affect

EFH for coho and Chinook salmon, specifically Southern Oregon / Northern California Coast

Coho and Upper Klamath-Trinity Rivers Chinook salmon.

of 63

Contents

I. Introduction ………………………………………………………………………… ....................... 4

II. Consultation To Date……………….…………………………………………..… .......................... 5

III. Proposed Action…………………………………………………………………. ............................ 6

IV. Description of Action Area, Analysis Area, Affected Species, Critical Habitat, Essential

Fish Habitat ……………………………………………………………….. ................................... 10

V. Existing Environment and Effects on Anadromous Fish and Their Habitat Indicators.... ............. 12

VI. Cumulative Effects—Endangered Species Act........................................................... .................... 30

VII. Cumulative Effects—National Environmental Policy Act................................................ .............. 30

VIII. Viability............................................................................................................................. .............. 31

IX. Project Elements and Effects Summary............................................................................ ............... 31

X. ESA Effects Determination............................................................................................... ............... 35

XI. Sensitive Species Effects Determination........................................................................... .............. 35

XII. Essential Fish Habitat Assessment................................................................................ .................. 35

Literature Cited………………………………………………………………………………………. ....... 37

Tables

Table 1. O'Neil Creek Pond Project 5th, 6

th, and 7

th-Field Watersheds and Hydrologic Unit

Codes…………………………………………………………………………........ .................... 4

Table 2. Action Area 7th-Field Watershed and Miles of Perennial and Seasonally Flowing

Streams................................................................................................................. ....................... 10

Table 3. Closest Distance between Project Activities and Pacific Salmonids, CH and EFH

Presence by 7th and 5

th Field Watershed ……………………………………………… ............ 16

Table 4. Indicators of Watershed Disturbance and Existing Condition …….....................……… .......... 21

Table 5. Indicators of Watershed Disturbance with Proposed Action...................... .................... ............29

Table 6. Summary of the effects on SONCC Coho salmon CH, SONCC Coho salmon and UKT

Chinook salmon EFH and KMP steelhead trout habitat of the O’Neil Creek Pond Project

for Project Element/Indicator combinations......................................... ................................. .....33

LIST OF APPENDICES: Supporting documents to this BA are located in the following Appendices:

• Appendix A: Map showing location of Project activities

• Appendix B: Best Management Practices and Project Design Features

• Appendix C: Klamath National Forest Matrix: Table of Population and Habitat Indicators for

Use on the Klamath National Forest in the Northwest Forest Plan Area

• Appendix D: Tables/Checklists for Documenting the Environmental Baseline and Effects of

Project(s) on Relevant Indicators for the Project

• Appendix E: Project Activities Within Riparian Reserves

• Appendix F: Life History and Biological Requirements of Pacific Salmonids

of 63

Biological Assessment / Biological Evaluation

for Threatened, Endangered, Proposed, and Sensitive Fish Species

That May be Affected by the O’Neil Creek Pond Project

January 9, 2012

I. INTRODUCTION

The purpose of this biological assessment/biological evaluation (BA) is to determine effects of the

Klamath National Forest’s (KNF) O’Neil Creek Pond Project (herein after referred to as the Project) on

anadromous fish species listed under the Endangered Species Act as Endangered or Threatened, on

designated Critical Habitat for those species, on species listed as “Sensitive” by the Pacific Southwest

Region of the USDA Forest Service.

The proposed project activities are located in the O’Neil Creek analysis area on the KNF, within the

Klamath River basin, California. The 5th-field, 6th field and 7th-field watershed names and hydrologic

unit codes (HUC) where project activities would occur are shown in Table 1.

Table 1. O’Neil Creek Pond Project 5

th, 6

th, and 7

th-Field Watersheds and Hydrologic Unit Codes

Watershed HUC

Seiad Creek-Klamath River (5th field) 1801020611

Bittenbender Creek-Klamath River (6th

field) 180102061103

O’Neil Creek (7th field) 18010206110303

This BA is prepared in accordance with legal requirements set forth under Section 7 of the Endangered

Species Act of 1973, as amended (ESA), [16 U.S.C. 1531 et. seq. 50CFR 402], Essential Fish Habitat

(EFH) consultation under 305 (b) (4) (A) of the MSA and is consistent with standards established in

Forest Service Manual direction (FSM 2672.42; USDA Forest Service 1991). The ESA fish species list

for this BA/BE was obtained online at http://www.nwr.noaa.gov/ESA-Salmon-

Listings/upload/snapshot0208.pdf, and the Sensitive species list is from the USDA Pacific Southwest

Region Sensitive Species List (USDA Forest Service 1998). This BA/BE analyzes effects on the

following Evolutionary Significant Units, designated critical habitat, and Essential Fish Habitat of

anadromous fish:

Endangered: None

Threatened: Southern Oregon / Northern California Coast (SONCC) Evolutionary

Significant Unit coho salmon (Oncorhynchus kisutch) and their designated

Critical Habitat

Proposed: None

Sensitive: Upper Klamath-Trinity Rivers Chinook salmon (O. tshawytscha) Klamath

Mountains Province steelhead trout (O. mykiss)

Essential Fish Habitat: SONCC coho salmon and UKTR Chinook salmon

Terms

O’Neil Creek Pond Project. All activities included in the proposed project.

Analysis Area. Includes the 7th Field watershed listed in Table 1. Also included is the Middle Klamath

of 63

River (in and immediately downstream of the project area), due to the presence of anadromous fish in and

downstream of the project area.

Action Area. The Action Area is defined (for ESA purposes) as “all areas to be affected directly or

indirectly by the Federal action and not merely the immediate area involved action” (50 CFR 402). The

Action Area for this BA/BE includes the 7th-field watershed where Project Elements would occur, plus

anadromous fish habitat downstream of where Project Elements would occur, to the point where Louie

Creek enters the Klamath River.

Project Elements. For ESA purposes, refers to the proposed habitat restoration treatments (and related

activities) in the O’Neil Creek Pond Project Assessment Area. See the section below titled, “Primary

Project Elements of the Proposed Action.”

II. CONSULTATION TO DATE

The O’Neil Creek Pond Project is consistent with the June 20, 1997, Biological Opinion issued

by NOAA Fisheries for the KNF Land and Resource Management Plan (LRMP), 1995 and the

April 16, 2001, NOAA Fisheries letter of response to re-initiation of consultation on the LRMP

based on SONCC coho salmon CH designation. Within the Incidental Take Statement for the

June 20, 1997, Biological Opinion for the LRMP, it is stated "NMFS based the reasonable and

prudent measures on a process for evaluating and screening proposed actions that are described

in the BAs. The evaluation and screening of proposed actions is accomplished through the ESA

consultation process developed to implement the May 31, 1995, Interagency streamlining

agreement and the Matrix of Pathway and Indicators from (USDI NMFS 1996). Interagency

Level 1 teams evaluate the effects of proposed actions against the environmental baseline at the

Project and watershed scales." The May 31, 1995, streamlining guidance was re-issued in 1997

and 1999; all versions describe the expected use of the "effects matrix" by Level 1 teams when

making ESA effects determinations and evaluating an action consistency with relevant LRMP

requirements.

The June 20, 1997, Biological Opinion for the LRMP identified Reasonable and Prudent

Measures on page 55 and Terms and Conditions on page 58, requiring the Forest to utilize the

Level 1 Team consultation process and apply the NOAA Fisheries Checklist and Matrix of

Pathways and Indicators (USDI NMFS 1996) to evaluate all proposed activities that may affect

listed, proposed, or candidate species of Pacific salmonids. Term and Condition 2b on page 59

states: "to facilitate the ESA consultation process and ensure agreement on effects

determinations, utilize the Level 1 process and apply the NMFS' Checklist and Matrix of

Pathways and Indicators (USDI NMFS 1996) to determine whether proposed actions are either

May Affect, Not Likely to Adversely Affect (NLAA) or May Affect, Likely to Adverse Affect

(LAA) listed, proposed, or candidate species of Pacific salmonids.”

The project was discussed with NMFS Fisheries staff on August 29, 2011, at a local Level 1

meeting. Since the effects determination for this project is “Not Likely to Adversely Affect” for

SONCC coho salmon and their CH, consultation with NMFS for this BA is required. This BA

was sent to Don Flickinger (NMFS) on December 5, 2011 for review. Comments were received

on December 14, 2011 and incorporated into the BA, which was returned to NMFS for final

review on January 4, 2012. NMFS did a final review of the BA and returned it to the KNF on

January 6, 2012. The BA was finalized on January 9, 2012.

of 63

III. PROPOSED ACTION

The purpose of the O’Neil Creek Pond Project is to: (1) create high quality off-channel winter

and summer rearing habitat for juvenile coho salmon; (2) create wetland habitat for other aquatic

animals and plants; and (3) improve access to lower O’Neil Creek and the off-channel pond for

coho salmon and other salmonids by removing one boulder and/or modifying an existing boulder

cascade in lower mainstem O’Neil Creek just above the Klamath River confluence.

The location of the project area is entirely on the floodplain of O’Neil Creek and the Klamath River –

near the confluence of O’Neil Creek with the Klamath River. During 25- to 50-year flood events and

larger, the entire project area is submerged beneath the swirling confluence waters of O’Neil Creek and

the Klamath River. The legal description of the O’Neil Creek Pond Project is:

T46N, R11W, SW corner of SW corner of Section 22 (Mt Diablo Meridian)

Restoration, enhancement, and creation of winter high-flow refugia and summer thermal refugia,

and access to these habitats is needed because these habitats are critical for maintaining and

restoring coho salmon populations that have been diminished due to road construction, upslope

land use, flood control efforts, historic industrial dredging, and floodplain reclamation on private

land. Similar off-channel ponds successfully constructed by the Mid Klamath Watershed

Council (MKWC) and the Karuk Tribe on private lands in the Seiad Creek watershed in 2010

were utilized by numerous juvenile coho salmon in winter 2010/2011, so juvenile coho use of the

O’Neil Creek off-channel pond is expected to be high. This project will help establish a trend

towards desired resource conditions.

This rest of this section describes each element of the project and describes the Project Design

Features that are incorporated into each project element to prevent or minimize adverse effects to

water quality and fish that could result from project implementation. The project also

incorporates Best Management Practices (BMPs) to protect water quality during project

implementation. BMPs and the specific measures that will be taken to comply with BMPs are

described in Appendix B.

Project Elements and Project Design Features

Project Element 1 (PE-1): Create additional off-channel pool habitat by enlarging and deepening

an existing shallow pond using an excavator.

The proposed project will enhance 6730 square feet of riparian wetland habitat, improve fish passage to

this habitat, and provide complex, high quality rearing habitat for coho salmon by enlarging and

deepening an existing shallow pond using an excavator. The existing pond habitat is very shallow and of

little to no habitat value for aquatic plants and fish. A 70,000 lb excavator will be used to construct additional pool habitat on the scoured, boulder-strewn

O’Neil Creek alluvial delta/Klamath River Floodplain, immediately downstream from the mouth of

O’Neil Creek and adjacent to the Klamath River. This will be done by excavating large boulders from the

floodplain of the Klamath River to extend, widen and deepen pond habitat connected to the alluvial delta

at the mouth of O’Neil Creek. The pond will be excavated to a depth as great as 6 feet. A shallow bench,

approximately one foot in depth, will also be excavated around the perimeter and along the northern

portion of the proposed pond to create shallow water habitat and to encourage growth of hydrophytic

vegetation, which is currently lacking.

of 63

Several large boulders will be left within the proposed pond to provide complexity and cover. Spoils

(boulders) from the excavation will be placed in linear rows along the edges of the created wetland habitat

to improve the potential for the created habitat to persist after large flood events (50-100 yr).

Access to the pond area (and the fish barrier area) by the excavator will require minimal disturbance of

dry site vegetation (removal of approximately 25 incense cedars (Calocedrus decurrens) less than 6”dbh.

These 25 trees are located more than 40 meters away from the wetted channel, and contribute no effective

canopy shade over the channel). Site access by the excavator will also involve running over a few

willows and small alders but these species will quickly recover within one year.

Project Design Features for PE-1 pond enlargement:

• Servicing and maintenance of the excavator will occur at least 200 feet from the wetted channels

of O’Neil Creek and the Klamath River.

• A Spill Prevention, Containment and Counter-Measures Plan, as outlined in BMP 2.12 (see

Appendix B), is required for this project due to the use of the excavator on the floodplain of

O’Neil Creek and the Klamath River.

• Pond excavation will take place during the summer low flow period between July 15 and October

15, when the proposed pond area is dry and is hydrologically-disconnected from O’Neil Creek

and the Klamath River, ensuring that suspended sediment mobilized by pond excavation site has

no means to enter the Klamath River.

• Wet Weather Operation Standards will be used to guide operations of the excavator during

periods of wet weather. Earth scientists will examine field conditions to determine when the soil

and/or access road have dried out enough to enable operations to resume without risk of

watershed impacts.

• Fish block-nets will be deployed when making the hydrologic connection between the newly

excavated pond and O’Neil Creek so that fish cannot enter the newly excavated pond until it has

filled and most of the suspended sediment has settled out of the water column. Water will be

flowing into the newly excavated pond from O’Neil Creek so there will be no turbidity entering

O’Neil Creek from the pond during excavation and little to no turbidity entering O’Neil Creek

from making the hydrologic connection after the pond is constructed. The inlet from O’Neil

Creek into the newly excavated pond will be constructed in such a way as to allow for fish

migration both into and out of the pond during all ranges of flows.

Project Element 2 (PE-2): Plant native riparian vegetation around the newly enlarged and

deepened pond.

Approximately 350 local native willow (Salix spp.), white alder (Alnus rhombifolia) and black

cottonwood (Populus trichocarpa) species will be hand planted using shovels and picks along the toe of

all pool banks for approximately 360 linear feet after the excavation is complete. Locally collected

cuttings and root plugs of the same species will be planted along the toe of the streambanks of each

channel of lower O’Neil Creek m and extend upslope approximately 10 feet (3 rows). Local willow

species may include, but are not limited to red willow (Salix laevigata), Pacific willow (Salix lucida ssp.

lasiandra), and narrow leaf (Salix exigua). During the first couple of years plants will likely be watered

by pumping water from the Klamath River following NMFS Water Drafting specifications (USDI NMFS

2001). Proposed revegetation is currently scheduled to take place during fall 201 1, while vegetation

monitoring will begin approximately one year after planting.

Following construction, all disturbed areas will be stabilized and reseeded with a native grass seed mix,

consisting of California blue-wild rye (Elymus glaucus), California brome (Bromus carinatus), California

poppy (Eschscholzia californica), Idaho fescue (Festuca idahoensis), meadow barley (Hordeum

brachyantherum), pine bluegrass (Poa secunda), Spanish clover (Lotus purshianus), three week fescue

(Vulpia microstachys), and tufted hairgrass (Deschampsia cespitosa).

of 63

Project Design Features for PE-2 riparian planting

• Only native riparian species will be planted

• NMFS Water Drafting specifications (NMFS 2001) will be followe when drafting water out of

the Klamath River for plant watering

Project Element 3 (PE-3): Remove a boulder and/or modify a boulder cascade to improve summer

fish passage into O’Neil Creek.

The excavator that deepened and enlarged the off-channel pond will also be used to remove a single

boulder and/or boulder cascade that is currently a partial juvenile fish passage barrier at the mouth of

O’Neil Creek, impeding juvenile salmonid access to cold water in O’Neil Creek during warm summer

months. The excavator will extend its arm over the O’Neil Creek channel to accomplish barrier removal

by removing one large boulder from the main channel and repositioning other boulders and cobble to

provide for easy fish passage. Figures 1-3 below show the boulder area causing the partial fish passage

barrier. The excavator bucket is the only part of the excavator that will contact the wetted channel, and

this location will be isolated with fish block netting to ensure that SONCC coho salmon are not present.

Project Design Features for PE-3 fish passage enhancement

• Servicing and maintenance of the excavator will occur at least 200 feet from the wetted channels

of O’Neil Creek and the Klamath River.

• A Spill Prevention, Containment and Counter-Measures Plan, as outlined in BMP 2.12 (see

Appendix B), is required for this project due to the use of the excavator on the floodplain of

O’Neil Creek and the Klamath River.

• Barrier removal using the excavator will take place during the summer low flow period

waterbetween July 15 and October 15 when lowest surface flows will ensure the least amount of

fine sediment mobilization.

• Wet Weather Operation Standards will be used to guide operations of the excavator during

periods of wet weather. Earth scientists will examine field conditions to determine when the soil

and/or access road have dried out enough to enable operations to resume without risk of

watershed impacts.

• Silt fencing will be placed downstream of barrier modification area to allow little/no suspended

sediment to enter any running water in O’Neil Creek or the Klamath River while barrier

modification is taking place.

• Fish block nets will be installed upstream and downstream from area where the fish passage

barrier is being modified to keep fish from entering the area being worked on by the excavator. A

Fishery biologist or fisheries technician will snorkel the exclusion zone to see if there are any

juvenile SONCC coho salmon inside the exclusion zone and , if so, barrier removal activities will

be postponed until it is determined that the fish are no longer present in the exclusion zone. If

juvenile SONCC coho salmon persist in the area, a block net will be installed at the upstream end

of the exclusion zone and pregressively moved downstream, to get the fish to move into the

refugial area downstream of the blocking net: outside of the exclusion zone.

• On hot days, if Klamath River water temperature remains consistently above 70 degrees F and

access to the thermal refugia at the mouth of O’Neil Creek become critical for salmonid survival

(as determined by a Forest Service or Karuk Tribe fisheries biologist), excavator work on the fish

passage barrier modification will be postponed and block nets will be removed, allowing juvenile

fish access to all available cold water areas.

Project Element 4 (PE-4): Installation and removal of fish block nets and silt fencing.

of 63

• Fish block-nets will be deployed when making the hydrologic connection between the newly

excavated pond and O’Neil Creek so that fish cannot enter the newly excavated pond until it has

filled and most of the suspended sediment has settled out of the water column to the bottom of the

pond. Water will be flowing into the newly excavated pond from O’Neil Creek so there will be

no turbidity entering O’Neil Creek from the pond during excavation and little to no turbidity

entering O’Neil Creek from making the hydrologic connection after the pond is constructed.

• Fish block nets will be installed upstream and downstream from area where the fish passage

barrier is being modified to keep fish from entering the excavation zone. Installing and removing

fish block nets causes negligible turbidity and/or disturbance of the streambed. A Fishery

biologist or fisheries technician will snorkel the excluded area to see if there are any juvenile

SONCC coho salmon inside the exclusion zone and , if so, project activities will be postponed

until it is determined that the fish are no longer present in the excluded area. If juvenile SONCC

coho salmon persist in the area, a block net will be installed at the upstream end of the excluded

area and progressively moved downstream to get the fish to move to a refugial site downstream

from the excavation zone.

• Silt fencing will be placed downstream of the barrier modification work area to allow little/no

suspended sediment to enter any running water in O’Neil Creek or the Klamath River while

barrier modification is taking place.

Project Design Features for PE-4 fish blocknets and silt fencing installation and removal

• Fish blocknets and silt fencing will be installed in a manner that causes the least streambed

disturbance

• Fish blocknets and silt fencing will be removed as soon as excavator operations are completed.

Excavator operation will cease and fish blocknets will be removed if water temperature in the

Klamath River consistently excedes 70 degrees F and fish need to access lower O’Neil Creel and

use the O’Neil Creek thermal refugia to survive. Silt nets will be removed in a manner in which

the captured sediment is not allowed to wash back into the stream.

Project Element 5 (PE-5): Water Drafting.

Water will be drafted from the Klamath River to water the riparian plantings along the edges of the pond

for the first two summers.

Project Design Features for PE-5 water drafting

• NMFS Water Drafting specifications (NMFS 2001) will be followed when drafting water out of

the Klamath River for plant watering

• Water will not be drafted out of O’Neil Creek or near the thermal refugia at the mouth of O’Neil

Creek

of 63

IV. Description of Action Area, Affected Species, Critical Habitat,

Essential Fish Habitat

Action Area— The Action Area is defined for ESA purposes as “all areas to be affected directly

or indirectly by the Federal action and not merely the immediate area involved in the action” (50

CFR 402). The Action Area for this BA is the O’Neil Creek 7th

field sub watershed where

project activities would occur, including the O’Neil Creek-Klamath River confluence area, the

floodplain area where pond construction is to occur, and the anadromous fish habitat adjacent to

and downstream from this sub-watershed in the Klamath River to Louie Creek (0.75 mile).

Table 2 gives the number of miles of perennial and seasonally-flowing streams in the O’Neil

Creek watershed.

Table 2. Miles of Perennial and Seasonally Flowing Streams in the O’Neil Creek

watershed.

7th-Field Watershed

Miles of

Perennial

Stream

Miles of

Seasonally

Flowing

Stream

Total Miles of

Stream

Channel

O’Neil Creek 3.5 4.25 7.75

The project area watershed is located in the Seiad Creek-Klamath River 5th

Field Watershed.

Affected Species and Presence of Critical Habitat—The following Pacific salmonid

Evolutionary Significant Units and their habitat in the Klamath River basin have special status

under the ESA or are given special management consideration as Forest Service Sensitive

species:

Endangered: None

Threatened: SONCC coho salmon

Critical Habitat: SONCC coho salmon

Proposed: None

Sensitive: Upper Klamath-Trinity Chinook salmon; Klamath

Mountains Province steelhead

Essential Fish Habitat: SONCC coho salmon; Upper Klamath-Trinity

Chinook salmon

The Bittenbender Creek-Klamath River 6th

field watershed provides approximately 30 miles of

anadromous fish habitat distributed within the main stem Klamath River, Walker Creek, O’Neil

Creek, Kuntz Creek, Mill Creek, Tom Martin Creek, and Negro Creek. Project effects are

expected to be confined to the O’Neil Creek-Klamath River confluence area, and approximately

0.75 mile downstream in the Klamath River to Louie Creek. Coho salmon use of O’Neil Creek

is confined to its confluence zone with the Klamath River.

of 63

Presence of anadromous salmonids and coho CH: The status and general life history of

anadromous salmonids potentially affected by the proposed action is in Appendix C. The distribution

of anadromous fish within the Analysis Area is shown in Appendix A. O’Neil Creek supports 0.9 miles

of habitat for steelhead trout, 0.012 mile of habitat for coho salmon, and 0.012 mile of habitat for

Chinook salmon, however, because the project is located at the mouth of O’Neil Creek, all three species

could be present in the project area. The Klamath River at the O’Neil Creek confluence and downstream

from there supports all three species as well. Conclusions regarding anadromous fish and their habitat

(including CH) occurrence are based on fish population surveys performed by the Forest Service, the

Karuk Tribe, and the Yurok Tribe. This distribution information is available on the Calfish.org

website, and it is considered current.

For the O’Neil Creek Pond Project, the estimate of SONCC coho salmon CH; SONCC coho

salmon and Chinook salmon Essential Fish Habitat (EFH) and KMP steelhead trout habitat in

the action area is as follows:

SONCC coho salmon CH

• O’Neil Creek – the lower 100 feet of O’Neil Creek.

• Klamath River – From the confluence with O’Neil Creek downstream to the confluence with

Louie Creek.

SONCC coho salmon and Upper Klamath-Trinity Chinook salmon EFH

• Klamath River – From the confluence with O’Neil Creek downstream to the confluence with

Louie Creek.

KMP Steelhead trout habitat

• Lower 0.9 mile of O’Neil Creek and from its confluence with the Klamath River downstream

to the confluence with Louie Creek.

of 63

V. EXISTING ENVIRONMENT AND EFFECTS TO

ANADROMOUS FISH AND THEIR HABITAT INDICATORS This section describes existing conditions and analysis of the direct and indirect effects of the project on

listed anadromous fish and their habitat (including critical habitat) at the site, and 7th and 5th-field

watershed scales. Habitat requirements (expressed by the key habitat Indicators) are similar for all

salmonids considered in this BA/BE. Existing conditions and effects are rated using criteria in

Appendix B, which summarizes the existing environment and effects for all Indicators, with data sources

identified.

The analysis of the potential effects on anadromous fish and their habitat is based on the proposed action

described in part III. The existing watershed conditions are described in the Fisheries Report for this

project (USDA Forest Service 2011). The location of anadromous salmonids is described below. The

habitat requirements (expressed by the Indicators) are similar for all salmonids considered in this BA.

Effects are rated using the Efficiency Measures section.

The analysis of the potential effects to anadromous fish and their habitat is organized by direct and

indirect effects and by effects to Indicators of anadromous fish habitat conditions. The Indicators

originate from Appendix A (Table of Population and Habitat Indicators) of the ‘Analytical Process for

Developing Biological Assessments for Federal Actions Affecting Fish within the Northwest Forest Plan

Area’ (USDA-USDC-USDI 2004),hereafter referred to as the AP. “Population characteristics” and

“Population and habitat” pathways listed in Appendix A of the AP were not evaluated for anadromous

fish since the AP states those pathways are for bull trout at this time. The population status of anadromous

fish species is discussed in Appendix C of this BA. The KNF used scientific data, field reviews, and

Cumulative Watershed Effects (CWE) modeling to determine the existing conditions for SONCC coho

salmon. The results are discussed below in the Efficiency Measures section.

Consideration of the intensity and extent of the proposed action as well as the proximity of anadromous

fish to proposed activities and the distribution and life history of anadromous fish (Appendix C) in the

Analysis Area assisted in making the final ESA effects determination for the Project. The proximity of

Project Elements (PEs) relative to anadromous fish and their habitat are described in Table 3. The Project

Elements considered for analysis include pond enlargement and deepening, riparian planting and

reseeding, fish barrier modification, silt-fence and fish blocknet installation, and water drafting.

For this BA, it is assumed that spawning, rearing, feeding, and migration can occur within all habitat occupied

by any of the ESUs of anadromous fish addressed in this document, unless otherwise stated. The probability for

short and long-term effects to anadromous fish is associated with direct effects to individual fish and effects to

instream habitat in the context of existing conditions.

O’Neil Creek supports anadromous habitat. The O’Neil Creek 7th field watershed within the Action Area

contains SONCC Coho salmon critical habitat at its confluence with the Klamath River, and there is no

documentation of use by Chinook salmon. O’Neil Creek does contain habitat for KMP steelhead trout

and steelhead trout have been documented in this watershed. The project area sub-watershed (7th field

watershed) transports flow, nutrients, sediment and other watershed products downstream to anadromous

habitat, therefore the O’Neil Creek 7th field watershed was analyzed in terms of potential effects to

anadromous habitat downstream of the project area.

At the site scale: Table 3 describes the shortest distance between PEs and occurrence of coho and

Chinook salmon and their CH and/or EFH, and the shortest distance between PEs and occurrence of

steelhead trout habitat. The project activities occur within SONCC coho salmon CH and EFH, and

steelhead trout habitat, in the lower 100 feet of O’Neil Creek and in the O’Neil Creek/Klamath River

confluence area. The project activities occur within Chinook salmon EFH in the O’Neil Creek/Klamath

of 63

River confluence area.

Streams at the 7th

field watershed scale: O’Neil Creek contains approximately 0.012 mile of Southern

Oregon/Northern California Coasts (SONCC) coho salmon CH (in the lower 100 feet of O’Neil Creek

and in the Klamath River confluence), no miles of habitat for Chinook salmon except at the Klamath

River confluence, and 0.9 mile of habitat for steelhead trout in O’Neil Creek and in the Klamath River

confluence.

Existing Condition and Effects Overview

Existing Condition of Anadromous Habitat:

O’Neil Creek provides regionally significant habitat for anadromous fishes, including SONCC Coho

Salmon (O. kisutch) at its confluence with the Klamath River , and KMP Steelhead (O. mykiss). Steelhead

may enter Project area tributaries, but no tributary streams have been designated as habitat for the species

(though the lower 0.20 mile of the unnamed tributary to O’Neil Creek is assumed to provide habitat for

steelhead in this analysis).

As mentioned above, O’Neil Creek sustains important refugial habitat for SONCC coho salmon. At

present, the refugial habitat within the project area appears to be in good condition, especially in terms of

water quality (i.e., little fine sediment). O’Neil Creek has been negatively impacted by flooding, private

land management activities, and past mining activities, and it is unclear the extent to which pools and/or

pool depth has been diminished as a result.

Less is known about Coho populations in O’Neil Creek, or the broader Klamath River system. NOAA

Fisheries in 2008 concluded that though information was lacking, available information indicates coho

populations are depressed. Using an adult-to-smolt relationship, CDFG projected very low abundances of

adult coho salmon returning to the Shasta River Basin in 2007 (249 adults), 2008 (30 adults), 2009 (9

adults), and 2010 (44 adults, Knechtle 2011). The assumption therefore, is that the trends in Coho

populations are basin or system wide, and numbers in O’Neil Creek and within the project area may have

also declined and remain depressed.

Effects Overview

Site Access: There will be minor vegetation and soil disturbance from mobilizing the excavator from

Highway 96 to the pond and fish barrier work-sites because: (1) the excavator will access the Klamath

River floodplain via an existing road so that only small overcrowded cedar trees will need to be removed,

(2) alders, willow and other wetland vegetation will be run over by the excavator but will not be killed or

removed and are expected to recover within a year or two, and (3) the excavator will cause negligible

disturbance on the Klamath River floodplain because this area is primarily large cobble, rock, and

boulders and has no to very sparse vegetation. There is negligible risk that erosion from disturbed ground

could enter a waterway because sufficient undisturbed ground or cobble/boulder river bar that separates

access route from waterways will prevent the overland flow of sediment. Water temperature will not be

affected because no vegetation that provides stream shading will be removed or run over by the

excavator. The Spill Prevention, Containment and Counter-Measures Plan that is required for this project

will minimize the risk of water contamination to a negligible level. Accessing the work-sites will not

increase road mileage or road density because an existing access road will be used and because driving

the excavator over riparian vegetation and the cobble-boulder river bar will not create a road or any

significant ground disturbance. None of the other salmonid habitat Indicators will be affected.

of 63

Pond Excavation: There will be no or negligible risk of turbidity or sedimentation entering O’Neil

Creek during pond excavation because pond excavation will take place during the summer low flow

period between July 15 and October 15 when the proposed pond area is dry and hydrologically-

disconnected from O’Neil Creek and the Klamath River. During hydrologic connection, water will be

flowing into the newly excavated pond from O’Neil Creek so there will be no or negligible risk of

turbidity or sediment entering O’Neil Creek during hydrologic connection. The inlet from O’Neil Creek

into the newly excavated pond will be constructed in such a way as to allow for fish migration both into

and out of the pond during all ranges of flows. The Spill Prevention, Containment and Counter-Measures

Plan that is required for this project will minimize the risk of water contamination to a negligible level.

Fish block-nets will be deployed when making the hydrologic connection between the newly excavated

pond and O’Neil Creek so that fish cannot enter the newly excavated pond until it has filled and most of

the suspended sediment has settled out of the water column. Therefore, there will be negligible risk of

fish injury or mortality from hydrologically-connecting the pond to O’Neil Creek following pond

excavation.

Riparian Planting and Reseeding: Riparian planting will cause negligible turbidity and sedimentation

to enter O’Neil Creek because this activity will be done by hand, will cause minor disturbance and nearly

all turbidity or sediment generated will settle out in the pond. Riparian planting will not affect stream

shading for the first few years but will increase stream shading and reduce water temperature in the long-

term. Riparian planting will help stabilize the streambanks of the pond and O’Neil Creek in the long-

term. Riparian planting will have no or negligible effect on the other salmonid habitat indicators.

Reseeding will have no effect on any of the indicators but could increase plant diversity on the river bar.

Fish Barrier Modification: Barrier removal using the excavator will take place during the summer low

flow period between July 15 and October 15 when the least amount of fine sediment will be entrained by

running water. Fish barrier removal will not add any sediment to the O’Neil Creek channel – only re-

arrange what is already there. Silt fencing downstream of fish barrier modification work-site will

minimize the amount of fines mobilized downstream. Turbidity will be increased during fish barrier

modification and for a few minutes to a few hours after work is completed. Turbidity will also be

increased during the first freshet of the wet season when the modified channel is likely to adjust to the

modification and become armored. Stream shading will not be affected because there are only willows on

site that provide little shade and only a small area of (about 40 by 40 feet) of willow will be run over.

The Spill Prevention, Containment and Counter-Measures Plan that is required for this project will

minimize the risk of water contamination to negligible level. None of the other salmonid habitat

Indicators will be affected.

There will be very low risk of injury or mortality of salmonids because: (1) Fish block nets will be

installed upstream and downstream from area where the fish passage barrier is being modified o keep fish

from entering area being worked on by the excavator. A Fishery biologist or fisheries technician will

snorkel the excluded area to see if there are any juvenile SONCC coho salmon inside the exclusion zone

and , if so, project activities will cease until it is determined that the fish are no longer present in the

excluded area. If juvenile SONCC coho salmon persist in the area, a block net will be installed at the

upstream end of the exclusion zoneand progressively moved downstream to get the fish to move to a

refugial site downstream from the excavation zone. And (2) on a hot day when the thermal refugia at the

mouth of O’Neil Creek becomes critical for salmonid survival (as determined by a Forest Service or

Karuk Tribe fisheries biologist), excavator work on the fish passage barrier modification will cease and

block nets will be removed - before water temperature in the Klamath River reaches critical levels for

salmonids. This will allow salmonids to use the thermal refugia at the mouth of O’Neil Creek.

Fish Blocknet and Silt Fence Placement and Removal: Installation of fish blocknets and silt fencing

will cause negligible turbidy and mobilization of streambed sediments because installation involves just

placing cobbles on the bottom of the net to hold it in place. Fish blocknets and silt fencing will block fish

of 63

passage but only during the few hours that the pond is filling and the fish barrier is being modified. Fish

blocknets will be removed if water temperature in the Klamath River reaches critically hot temperatures

and fish need to access O’Neil Creek to use the entire O’Neil Creek thermal refugia to survive. Fish

blocknet and silt fencing installation and removal will have no effect on any of the other salmonid habitat

Indicators.

Water Drafting: Water drafting to water planted riparian vegetation around the pond will not adversely

affect salmonids because: (1) drafting will be done in accordance with NMFS Water Drafting

specifications (NMFS 2001), and (2) water will not be drafted out of O’Neil Creek or near the thermal

refugia at the mouth of O’Neil Creek. Water drafting will have negligible effect on water temperature

because warm water out of the Klamath River will be drafted – not cool water. Water drafting will have a

negligible effect on flow in the Klamath River. Water drafting will have no effect on any of the other

salmonid habitat indicators.

Direct Effects to anadromous fish and habitat:

Direct effects to SONCC coho salmon are expected to be insignificant for the following

reasons:

(1) Fish block nets will be installed upstream and downstream from area where the fish passage

barrier is being modified o keep fish from entering area being worked on by the excavator. A

Fishery biologist or fisheries technician will snorkel the excluded area to see if there are any

juvenile SONCC coho salmon inside the exclusion and , if so, project activities will cease until it

is determined that the fish are no longer present in the excluded area. If juvenile SONCC coho

salmon persist in the area, a block net will be installed at the upstream end of the excluded area

and slowly moved downstream to get the fish to move out of the area to a refugial site

downstream from the excavation zone.

(2) On a hot day when the thermal refugia at the mouth of O’Neil Creek becomes critical for

salmonid survival (as determined by a Forest Service or Karuk Tribe fisheries biologist),

excavator work on the fish passage barrier modification will cease and block nets will be

removed - before water temperature in the Klamath River reaches critical levels for salmonids.

This will allow salmonids to use the entire thermal refugia at the mouth of O’Neil Creek.

(3) Fish blocknets and silt fencing will block fish passage but only during the few hours that the pond

is filling and the fish barrier is being modified. Fish blocknets will be removed if water

temperature in the Klamath River reaches critically hot temperatures and fish need to access

O’Neil Creek and use the O’Neil Creek thermal refugia to survive.

(4) Water drafting will not adversely affect salmonids because: (1) drafting will be done in

accordance with NMFS Water Drafting specifications (NMFS 2001), and (2) water will not be

drafted out of O’Neil Creek or near the thermal refugia at the mouth of O’Neil Creek.

Proximity and Probability: See Table 3 for proximity of PEs to anadromous fish and their

habitat.

of 63

Table 3 – Closest Distance between Project activities and Pacific Salmonids, CH and EFH Presence by

7th

and 5th

Field Watershed

Watershed Name

(Level)

Stream Name

(s)

Distance to CH and EFH

(miles/activity)

Distance to Habitat occupied by

Steelhead Trout (miles)

O’Neil Creek (7th

field)

O’Neil Creek 0.00 – Pond Enlarging1

0.00 – Riparian Planting /

Reseeding

0.00 – Fish Barrier Modification2

0.00 – Blocknets and Silt Fencing

0.00 – Water Drafting

0.00 – Pond Enlarging1


Reseeding




Seiad Creek-

Klamath River

(5th field)

O’Neil Creek

Klamath

River



Reseeding






Reseeding




1 = Pond will be hydrologically-disconnected from fish habitat during excavation.

2 = Fish blocknets will exclude salmonids from fish passage modification work-area.

Indirect Effects to anadromous fish and habitat The analysis of indirect effects is organized by habitat Indicators. As mentioned earlier, the

fisheries analysis uses key Indicators of habitat quality (habitat Indicators) as identified through

the Analytical Process (USDA-USDOC-USDI 2004). The following habitat indicators will be

discussed further in this document. They are:

• Water Quality: Stream Temperature, Chemical Contamination

• Water Quality and Habitat Elements: Suspended Sediment and Substrate Character, Large

Woody Debris, Pool Frequency and Quality, Streambank Condition, Floodplain

Connectivity, Off-channel Habitat, Refugia

• Flow/Hydrology: Change in Peak/Base Flow

• Watershed Condition: Riparian Reserves, Disturbance History and Disturbance Regime

Habitat Indicator: Water Quality—Stream Temperature

Existing Conditions Water temperature in O’Neil Creek is properly functioning based on professional judgment and

the overall condition of the riparian reserves upstream on the project area. O’Neil Creek does

provide important coldwater refugia habitat at its confluence with the mainstem Klamath River.

Post-Project Condition Stream temperatures are not expected to be increased as a result of the proposed action. This

assessment is based on the location of the proposed pond and the project activities. The most

likely impact to stream water temperatures would occur if vegetation that provided shade to

O’Neil Creek was removed. Although some vegetation that provides shade to O’Neil Creek may

be disturbed during construction of the pond, no vegetation that provides shade to O’Neil Creek

is expected to be removed Access to the pond area (and the fish barrier area) by the excavator will

require minimal disturbance of dry site vegetation (removal of approximately 25 incense cedars

(Calocedrus decurrens) less than 6”dbh. These trees are located more than 40 meters away from the

of 63

wetted channel, and contribute no effective canopy shade over the channel). The result should be

minimal reduction of shade in the short term.


cottonwood (Populus trichocarpa) species will be planted along the toe of all pool banks for

approximately 360 linear feet. Locally collected cuttings and root plugs will be planted 5 feet

apart along the toe of each stream bank and extend upslope approximately 10 feet (3 rows). This

will provide additional future shade along the banks of the pond.

Any increase in stream temperature in O’Neil Creek during the summer months resulting from

the creation of the 6730 square foot pond would be very localized due to the proximity of the

pond from the mouth of O’Neil Creek and due to the fact that water will flow into the pond from

O’Neil creek but not out of the pond back into O’Neil Creek . No increase in stream temperature

is expected from the removal of the boulder cascade barrier because there are only willows on site

that provide little shade and only a small area of (about 40 feet by 40 feet) of willow will be run over by

the excavator. These willows will grow back quickly after completion of project activities. The

addition of shaded, cool water flowing into this section of O’Neil Creek from upstream of the

project area will result in neutral temperature-related effects to SONCC coho salmon CH and

anadromous fish habitat.

Habitat Indicator: Water-Quality, Chemical Contamination

Existing Condition

Chemical contamination has not been identified in the Action Area, nor are any point sources of

contamination known. Portions of the west bank of the Klamath River within the project area

have been mined. Recent evaluations of California mining (in the Sierra Nevada) have found

that some mined areas have residual mercury contamination. Mercury was commonly used

during mining operations to extract and process gold. There is no documentation of mercury

contamination in the Project area, but inventory of this potential problem has not been

conducted.

Post-Project Condition and Indicator Summary The sources for chemical contamination from Project activities are related to spills associated

with refueling or equipment failure of the excavator that will be used for constructing the pond

and boulder cascade removal.

Refueling and maintenance of motorized equipment will occur at least 200 feet away from any

channel. BMP 2.12 (Appendix D) will guide all fueling and lubricating actions and, in particular,

fuel containment systems will be in place as necessary. The Spill Prevention, Containment and

Counter-Measures Plan that is required for this project will minimize the risk of water contamination to

negligible level . Therefore, no effects are expected at the site of operations of the Project, or at

the 7th

or 5th

field scale.

Habitat Indicator: Habitat Access - Physical Barriers

Existing Condition There are no human-made barriers present in the Project Area.

of 63

Post-Project Condition and Indicator Summary There is a boulder cascade barrier at the mouth of O‘Neil Creek that currently impedes juvenile

salmonid access to O’Neil Creek during the warm summer months. It is not a complete barrier

however. The excavator will be used to remove this boulder cascade barrier at the mouth of

O’Neil Creek. It is a natural barrier that has been observed to form every summer since 2006 as

flows drop in the mainstem Klamath River. As the following photos show, passage during late

spring is excellent, but by early summer when coho are most actively seeking out summer

refugia, the barrier is beginning to form.

Figure 1. Photo taken May 25, 2010, when Klamath mainstem flows are elevated. The braid on

the left side of the photo becomes the only channel later in the season, and the boulder over

which it pours is proposed for removal.

of 63

Figure 2. Photo taken June 28, 2007, showing same area as Figure 1, but with decreased Klamath

mainstem flows. Shallow jump pool depths paired with higher cascade jump height makes this a

partial barrier for coho juveniles seeking summer thermal refugia.

of 63

Figure 3. Photo taken July 25, 2011, showing same area as Figures 1 and 2, with increased jump

height and boulder to be removed.

of 63

Figure 4. Photo taken July 25, 2011, showing the mouth of O’Neil Creek on the left and Klamath

River habitat immediately downstream from the mouth.

Other than this partial barrier that will be removed, project activities will not directly alter

existing fish habitat access.

Habitat Element- Suspended Sediment- Substrate

Existing Condition Suspended sediment-substrate information from O’Neil Creek is limited.

Road densities within the project area are listed below. Table 4. Indicators of Watershed Disturbance and Existing

Condition

Watershed Acres ERA TOC Rd Density*

O’Neil Creek 2,429 0.42 8.0% 2.8

The types and levels of watershed disturbance also provide evidence of potential sediment

production and delivery. Disturbance in the project area was estimated from historic timber sale

maps and a GIS road layer. The Klamath NF CWE process, based on the Region 5 Equivalent

Roaded Acres (ERA) method was applied. Treatment coefficients were applied to disturbed

of 63

areas (roads equal 1.0, light timber harvest equals .1, etc.). Road densities are expressed in miles

of road/square mile*. These roads include open, closed, and other unclassified roads. The percent

ERA of each project area sub-watershed are presented in Table 4. Also included in Table 4 is the

existing threshold of concern (TOC) for ERAs in these watersheds.

Road densities in the O’Neil watershed are moderate. Road location in this watershed relative to

stream channels is considered a low risk for causing sedment mobilization to stream channels.

The overall level of disturbance in this watershed (as expressed by ERA) is moderate. This level

of disturbance represents a low to moderate risk of elevated sediment delivery. The values are

well below the TOC for this watershed. The TOC value is based on watershed sensitivity factors

such as steepness of slopes, soil properties and aquatic ecosystem values.

Much of the portion of O’Neil Creek within the project area was historically impacted by

hydraulic and suction mining.

Post-Project Condition

The risk of increased surface erosion from project activities is low. Although project activities

do occur within RRs, the limited/localized scale of the Project, and site specific resource

protection measures and BMPs would minimize the sediment delivery potential resulting from

pond construction, silt fencing, damage to existing vegetation, temporary access road

construction and removal, and boulder cascade removal. The risk of accelerated sediment

delivery associated with an increase in mass wasting is also rated as low.

Project activities involving use of the excavator have low potential to remove ground cover to

the extent where the erosion hazard would be increased due to cobble, rock, and boulders being

the dominant cover (>80%) and that the vegetation that is to be removed is not adjacent to wetted

stream channels. Post-treatment riparian planting around the pond will provide enhanced

vegetation to maintain adequate groundcover following project activities. Given high ground

cover expected to result from the riparian planting, the primary risk of erosion and sediment

delivery would be from excavating large boulders from the floodplain of the Klamath River to

extend, widen and deepen pond habitat within the alluvial delta near the mouth of O’Neil Creek,

and from removing the boulder cascade at the mouth of O’Neil Creek. By following Project

design features and BMPs, the risk of increased erosion on site is low: strengthened by the fact

that the pond site will have no surface connection to wetted channels during construction, and

that there will be little fine sediment disturbance at the boulder barrier removal site.

Although some sediment delivery into O’Neil Creek is possible from pond construction and

barrier removal, sediment delivery is expected to be minimal for the following reasons.

Project activities will occur during the dry season when the proposed pond area is dry, and silt

fencing will be placed at the inlet of the proposed pond to minimize any potential suspended

sediment from entering any flowing water in O’Neil Creek or the Klamath River. Removal of at

least one boulder at the mouth of O’Neil Creek will input minimal sediment into the Klamath

River due to the lack of fine materials and minimal work to be done there.

of 63

Site access by the excavator will require minimal disturbance of dry site vegetation (removal of

approximately 25 incense cedars (Calocedrus decurrens) less than 6”dbh). Site access by the

excavator will run over willow and small alders but these species that are expected to quickly

recover within one year. Any areas disturbed by the excavator will be stabilized and reseeded

with a native grass seed mix (see the paragraph below).

The pond construction site area has little or no fine textured soil present so little or no fine

sediment is expected to be mobilized during pond construction activities.

Spoils (boulders) from the excavation will be placed in linear rows along the edges of the created

wetland habitat to improve the potential for created habitats to persist after large flood events

(50-100 yr). These areas will be stabilized and reseeded with a native grass seed mix and

replanted with native willow, alder and black cottonwood (see the next two paragraphs).

Following construction, all disturbed areas will be stabilized and reseeded with a native grass

seed mix, consisting of California blue-wild rye (Elymus glaucus), California brome (Bromus

carinatus), California poppy (Eschscholzia californica), Idaho fescue (Festuca idahoensis),

meadow barley (Hordeum brachyantherum), pine bluegrass (Poa secunda), Spanish clover

(Lotus purshianus), three week fescue (Vulpia microstachys), and tufted hairgrass (Deschampsia

cespitosa).





will provide additional future bank stabilization along the banks of the pond.

Water drafting sites for watering plants for up to two years following completion of project

activities will occur at designated sites for that purpose. Erosion-control measures will be

employed at the sites to prevent water leakage from causing stream sedimentation. Hazardous

material spill prevention and containment equipment will be present on site. Pumping equipment

will be in a well-maintained condition, free of fluid leaks, and have hoses in good operating

condition.

Indicator Summary for Water Quality: Suspended Sediment-Turbidity-

Substrate character

The project activities will have an insignificantly negative effect on this Indicator. Sediment

delivery from project activities is expected to be minimal. While some sediment from project

activities may reach streams and other aquatic habitats when the boulder cascade barrier at the

mouth is removed, the increase would not be measurable (See Appendix E).

BMP monitoring conducted on the KNF over the past 10 years has indicated that BMPs have

both a high level of successful implementation and effectiveness. See the following link to BMP

monitoring on the KNF website.

http://www.fs.usda.gov/detail/klamath/landmanagement/resourcemanagement/?cid=stelprdb5312

713

of 63

Indicator Summary for Habitat Elements: Substrate

Character/Embeddedness

The project activities will have an insignificantly negative effect on this Indicator. Sediment

delivery from project activities is expected to be minimal and last no more than a few hours

when silt fencing is removed and then when the first fall freshet occurs. While some sediment

from project activities may reach streams and other aquatic habitats, the increase is not expected

to be measurable (See Appendix E).

Habitat Element – Large Woody Debris (LWD)

Existing Condition

Generally, riparian reserves throughout the project area are rated as at risk. The lower 0.5 mile of

O’Neil Creek has been impacted by hydraulic mining. The portion of the Klamath River

floodplain within the project area contains no large live trees since it consists almost entirely of

boulders, rock, and cobble and has very little soil available for growth of large trees. For these

reasons, large wood recruitment is rated as at risk. No large wood data is available for the portion

of O’Neil Creek and its tributaries upstream of the project area, so assessment of conditions is

based primarily on professional judgment.


The removal of approximately 25 incense cedars (Calocedrus decurrens) located more than 40

meters from the creek channel, and that have small diameters (less than 6”dbh) will not

contribute to LWD recruitment, while Project planting of trees is expected to recruit more

woody debris over the long term.

Indicator Summary for Habitat Elements: Large Woody Debris

LWD will not be affected by project activities because the project activities will not remove

large trees. Neutral effects to this indicator are expected in the short term.

Habitat Elements - Pool Frequency and Quality

Existing Condition

This Indicator relates to frequency and quality of primary pools. This Indicator is applicable to

streams containing SONCC coho CH that may be affected by the proposed project activities.

These are limited to the lower 0.25 miles of O’Neil Creek, and the portion of the Klamath River

from the confluence with O’Neil Creek to approximately 0.75 miles downstream to the

confluence with Louie Creek. Based on professional judgment, existing pool frequency for

O’Neil Creek seems to be functioning at potential, though the pools are typically shallow.


of 63

Project activities will have a neutral effect on pool frequency and quality because the processes

that affect them will not be measurably changed. As discussed under those elements, the project

is not expected to alter flow regimes or sediment delivery to channels. As a result, bedload and

fine sediment deposition, and the frequency and size of scour events should remain as they

currently exist. As a result, pool frequency and depth should also remain unchanged, subject to

the influences of large flood events and drought.

Indicator Summary for Habitat Elements: Pool Frequency, Large Pools, Pool

Quality

Project activities will have a neutral effect on pool frequency and quality because the processes

that affect them will not be measurably changed. However, the Project will create a pool in the

Klamath floodplain that will enhance rearing opportunities for juvenile salmonids, including

SONCC coho salmon.

Habitat Indicators – Channel Condition and Dynamics;

Streambank Conditions

Average Wetted Width to Maximum Depth Ratio

Existing Conditions

Based on field reviews, streambank conditions in the O’Neil Creek7th

field watershed appear to

be in functioning condition. Channel width to depth ratios appear to be appropriate for the

catchment size, channel gradient, and composition.


The project activities would maintain channel integrity and processes. Channels and stream

banks would not be damaged by mechanical equipment. Large wood delivery would not be

affected (see discussion of Large Woody Debris).

Due to the limited amount of project activities, occurring along 10 to 15 feet of the O’Neil Creek

channel, such changes are not expected to be measurable at either the local or the watershed

scale. Peak flows are not likely to be increased, so increased channel cutting is not anticipated.

Indicator Summary for Channel Condition/Dynamics: Streambank Condition

The proposed action will have a neutral effect on this Indicator.

Habitat Indicator: Floodplain Connectivity

Existing Conditions

Stream channels in the O’Neil Creek 7th

field watershed are typically steep and with little

floodplain development. O’Neil Creek displays little or no true floodplain, except at its

confluence with the Klamath River. In terms of connectivity, channels do not display

of 63

downcutting. Flood interaction with near stream environments appears to be similar to that with

which the system has evolved since gold mining ended.

Post Project Condition

Floodplain connectivity in the Action Area should not change because of project activities. The

project will not directly impact streams or channel banks, and no changes to the size, timing or

frequency of peak flow events, including events greater than bank full, are expected.

Indicator Summary for Channel Condition/Dynamics: Floodplain

Connectivity

Considering the effects of all project elements on this Indicator, the proposed action will have a

neutral effect on this Indicator.

Habitat Elements – Off-channel habitat

Existing Condition

Off-channel habitat is not a significant component in the steep channels of the O’Neil Creek 7th

field watershed. Although there is limited off channel habitat, it is considered “Properly

Functioning” because the channel morphology (steep channel gradients) does not naturally

provide for greater off channel habitat potential.

Post-Project Condition and Indicator Summary

Project activities will not affect the limited off channel habitat in the short term, because

potential sediment delivery to channels from Project-related surface erosion is low, the risk of

mass wasting is not significantly increased by PEs, and alterations in the flow regime are not

expected to be measurable at any scale.

Effects to this Indicator are neutral in the short term and positive in the long term along the

Klamath River, due to construction of the new off-channel pond which will increase the quality

and quantity of mainstem Klamath River off-channel rearing and overwintering habitat available

for juvenile SONCC coho salmon, UKT Chinook salmon and KMP Steelhead trout.

Habitat Elements – Refugia

Existing Condition

The Northwest Forest Plan identified Key Watersheds to create a system of large refugia

comprising watersheds that are crucial to at-risk fish species and stock and provide high quality

water (NFP ROD, B-12). Seiad Creek-Klamath River is not a Key Watershed. The perennial

stream in the project area (O’Neil Creek) provides cold-water refugia cold water to the Klamath

River.

of 63

Post-Project Condition and Indicator Summary:

Because no significant changes in stream temperature are expected to result from the project

activities, there will be no change in the temperature based refugia characteristics of the project

area watershed.

Habitat Indicator: Flow/Hydrology—Change in Peak/Base Flow

Existing Conditions

Pre-project Peak/Base Flow conditions are Properly Functioning for the O’Neil Creek 7th

field

watershed. Recent road improvement work has improved drainage and reduced the influence of

the road system in this 7th

field watershed on storm flows. Field inspections of O’Neil Creek as

well as seasonal observation of flowing channels in the project area revealed no evidence of

accelerated channel cutting.

Post Project Condition

There is a low risk in changes in peak flow from project activities. Since this area on the

Klamath River floodplain is primarily large cobble and boulders and there is very little fine

textured soil present, the project activities should not measurably increase soil compaction.

Therefore runoff at the site scale should not be significantly increased.

Removal of vegetation associated with the project activities is not likely to affect peakflows.

Indicator Summary for Flow/Hydrology: Changes in Peak and Base Flows

The project activities will have will have a neutral effect on this Indicator.

Habitat Indicator: Watershed Condition – Riparian Reserves

Existing Condition

Generally, riparian reserves throughout the project area are rated as at risk. The lower 0.5 miles

of O’Neil Creek has been impacted by hydraulic mining. The portion of the Klamath River

floodplain within the project area contains no large live trees due to that the floodplain consists

almost entirely of boulders and cobble and has very little soil available for growth of large trees.


The project activities will not impair RRs ability to buffer sediment. Running over some riparian

vegetation with an excavator when affecting barrier removal along 10 to 15 linear feet of lower

O’Neil Creek will not redue effective stream shade significantly. Large woody debris

recruitment to streams will also not be affected. Appendix E summarizes the activities that are

scheduled to occur in RRs.

of 63

Project activities involving use of the excavator have low potential to remove ground cover to

the extent where the erosion hazard would be increased. Post-treatment riparian planting around

the pond will provide enough vegetation to maintain adequate groundcover following project

activities. Given high ground cover expected to result from the riparian planting, the primary risk

of erosion and sediment delivery would be from excavating large boulders from the floodplain of

the Klamath River to extend, widen and deepen pond habitat connected to the alluvial delta at the

mouth of O’Neil Creek, and from removing the boulder cascade barrier. If BMPs are applied,

the risk of increased erosion on site is low; with RRs serving as buffers, the risk of sediment

delivery to channels is very low.

Site access by the excavator will require minimal disturbance of dry site vegetation (removal of

approximately 25 incense cedars (Calocedrus decurrens) less than 6”dbh). Site access by the

excavator will run over willow and small alders but these species will quickly recover within one

year. Any areas disturbed by the excavator will be stabilized and reseeded with a native grass

seed mix (see the paragraph below).

Spoils (boulders) from the excavation will be placed in linear rows along the edges of the created

wetland habitat to improve the potential for created habitats to persist after large flood events

(50-100 yr). These areas will be stabilized and reseeded with a native grass seed mix and

replanted with native willow, alder and black cottonwood (see the next two paragraphs).

Following construction, all disturbed areas will be stabilized and reseeded with a native grass



meadow barley (Hordeum brachyantherum), pine bluegrass (Poa secunda), Spanish clover

(Lotus purshianus), three week fescue (Vulpia microstachys), and tufted hairgrass (Deschampsia

cespitosa).





will provide additional future bank stabilization along the banks of the pond.

Indicator Summary for Watershed Condition: Riparian Reserves

In summary, considering activities proposed within RRs, the condition of the RRs, and the

connection of RR condition to downstream anadromous habitat and based on above discussions

of the other Indicators in Section V, there will be insignificant negative effects to RRs from

project activities in the short term and long term positive effects. Due to the proximity of this

rearing habitat to the mouth of the Scott River, increased rearing success and resulting increased

smolt to adult survival of Scott River coho salmon, and other non-natal rearing of other coho

juveniles, will likely have long term positive effects on coho populations in the Scott River and

other upstream Klamath tributaries.

Habitat Indicators: Watershed Condition – Disturbance History and

Disturbance Regime

of 63

Existing Condition

As with most forested watersheds in the west, the ecology of O’Neil Creek is strongly influenced

by two primary disturbance elements, fire and flooding. Major floods occurred in 1964 and most

recently in 1997, and play a large role in channel for and age and structure of riparian

communities. Major precipitation events also serve to trigger mass wasting events that are key

watershed processes in the basin.

The second natural disturbance mechanism affecting the O’Neil Creek watershed is wildfire. Fire

helped shape the vegetation of the Klamath Mountains, and the effects of the natural fire regime

strongly influenced the O’Neil watershed and aquatic habitats through effects on flow and

sediment regimes, including, with flood events, the timing and location of debris flows.

Unfortunately, decades of well intended fire suppression activities, and a change in climate, have

altered the historic fire regime. Currently, fires typically burn with a higher percentage of high

intensity and high severity than that which occurred historically. The result is larger fires that

reach the crown and cause mortality to much of the vegetation, including large, thick barked

conifers able to survive fires of lower intensity. Significantly, fires now burn riparian and stream

side vegetation at high intensity and high severity. Such fires can affect large portions of a

watershed, including sensitive streamside zones and seriously alter hydrologic processes. These

changes in sediment and flow regime, stream shading and large wood recruitment are transported

downstream, eventually affecting the condition of anadromous habitat.

At the 7th

field watershed scale, attributes calculated to model cumulative watershed effects

(CWE) on the KNF are helpful in describing the amount of disturbance from past management

activities. These activities have removed ground cover and altered flow patterns and timing, and

have the potential to adversely affect these processes downstream, and by extension, adversely

affect anadromous habitat in O’Neil Creek.

The KNF CWE process describes the current landscape conditions for ERA/TOC (flow effects

analysis), USLE (surface erosion), and GEO (mass wasting) that are based on an accounting of

past disturbances. All three models are used to describe the level of existing watershed

disturbance in the O’Neil 7th

field watershed in the project area. Results are presented in Table 5.

The metrics presented in the tables indicate that roads are primary existing disturbance of

concern, because the level of overall disturbance is low. Due to the small and limited scale of

this project, an actual CWE model run was not considered warranted, as no change in parameter

values would be detactable. Therefore only model results for existing condition are shown.

The condition of sensitive landforms has a great influence on the condition of aquatic habitats. In

the O’Neil Creek watershed, the most important of these landforms are areas in inner gorges and

other streamside zones, and lands prone to mass wasting. In general, these areas have been

excluded from management over the past few decades, and include relatively low road density,

and very few landings and other sites of compaction. In terms of sediment production buffering

and provision of shade and woody debris, these are in excellent condition.

of 63

Table 5. Indicators of Watershed Disturbance with Proposed Action

Watershed

Road Density

(mi/sq mi) ERA GEO (risk ratio)

USLE (risk

ratio)

current TOC current current current

O’Neil Creek 3.8 8.0% 0.42 0.55 1.10

Bittenbender

Creek-

Klamath River

(6th Field)

4.3 8.8% 0.32 0.61 0.60

Seiad Creek-

Klamath River

(5th

Field)

4.6 8.1% 0.27 0.47 0.40

Post Project Condition After consideration of the past conditions and site level review by the hydrologist, no adverse effects to

flows are expected in the O’Neil Creek 7th field watershed or the Bittenbender Creek-Klamath River 6

th

field watershed (USDA Forest Service 2011).

Analysis concluded that project activities would not have a measureable effect on watershed condition

(disturbance and regime) due to the localized nature of the project and insignificant channel alteration;

therefore there no affect on flooding is anticipated (USDA Forest Service 2011).

Therefore, neutral effects to this indicator are expected.

Indicator Summary for Watershed Condition: Disturbance History and

Regime

The project activities will have a neutral effect on this Indicator.

VI. Cumulative Effects—Endangered Species Act

The ESA defines cumulative effects in 50 CFR 402.02 as “those effects of future State or private

activities, not involving Federal activities that are reasonably certain to occur within the action area of the

Federal action subject to consultation.”

The O’Neil Creek Pond Project would create a pond of approximately 6730 square feet in size within the

O’Neil Creek 7th field watershed of about 2,429 acres, and will remove a partial barrier to juvenile

salmonid fish passage at the mouth of O’Neil Creek. O’Neil Creek has about 0.012 mile of SONCC coho

salmon habitat CH and EFH, 0.01 miles of UKTR Chinook salmon EFH, and 0.8 miles of KMP steelhead

trout habitat. The project area has about 0.10 mile of SONCC coho salmon habitat CH and EFH, 0.01

miles of UKTR Chinook salmon EFH, and 0.10 miles of KMP steelhead trout habitat. Reasonably

foreseeable future actions in the project area include prescribed fire to maintain fuel loadings at

acceptable levels. These actions have a low potential to increase sedimentation into these streams because

they would likely consist of underburning and removal of small-diameter trees for fuels reduction along

access roads.

of 63

VII. Cumulative Effects—National Environmental

Policy Act

Evaluation of cumulative effects for watershed condition, aquatic and riparian species, and habitat is

evaluated at the sub-watershed scale. Additionally, potential cumulative effects at the O’Neil Creek scale

are considered, due to the presence of anadromous fishes in and downstream of the project area.

Past, present, and ongoing activities within the O’Neil Creek Pond project area and O’Neil Creek that

may contribute to cumulative effects on watershed and aquatic resources include: past mining activities,

past timber activities, the transportation system (unhealed roads, road crossings, and skid trails),

recreation (degradation of localized riparian areas from excessive camping or motorized vehicle use),

prescribed fire, and wildfire. Collectively, these activities may contribute excessive fine sediment or

otherwise alter water quality into downstream reaches.

The proposed action was designed to minimize potential adverse effects to the O’Neil Creek watershed, in

recognition of current watershed condition, project area aquatic resources and anadromous fish habitat.

The integrated design features and other portions of the proposed action should minimize the risk of

potential erosion and sedimentation. Because of this, there is a very low risk that the proposed action

would contribute toward adverse cumulative watershed effects. Although project activities will occur

within the RRs, in the long term they will improve riparian function and meet ACS objectives.

The KNF Schedule of Proposed Actions was reviewed to identify current and reasonably foreseeable

future projects in the O’Neil Creek watershed that should be included in the cumulative effects analysis

for the O’Neil Creek Pond project. There are no major projects in the planning stage. Ongoing projects

include annual road maintenance, dispersed recreation, hiking, and appropriate responses for fire

suppression. It is likely that prescribed fire to maintain desirable fuels conditions will also be undertaken

periodically.

The CWE assesses the risk of adverse effects on erosion, geologic stability, and flows. The results of the

modeling are summarized in Table 5. The results include only existing condition (reflecting past and

existing disturbance) for the various model components attributes since a CWE run was not able to be

completed for this project due to the small size of the project.

The O’Neil Creek 7th field watershed has a risk ratio just over 1.0 for the USLE Risk modeling at 1.1,

placing it at a moderate threshold of risk. The increase in CWEs from project implementation is

considered too small to detect by modeling.

Under existing conditions, neither the Bittenbender Creek-Klamath River 6th field watershed or the Seiad

Creek-Klamath River 5th field watershed are over threshold for surface soil erosion, mass-wasting, or

equivalent roaded area. As importantly, road densities would not be changed. There are no expected long-

term cumulative effects on water quality or aquatic habitat or populations. It is expected that aquatic

habitat quality would be improved in the long term as a result of project implementation.

VIII. Viability

Chinook salmon and steelhead trout are listed as Forest Service Sensitive species in Region 5.

Implementation of the KNF LRMP Standards and Guidelines, which are designed to reverse the trend of

habitat degradation, as well as address long-term persistence of late-successional-dependent species,

would primarily contribute towards species viability. Overall, implementation of the project would help

maintain the health of forested ecosystems by increasing access to habitat by barrier removal and

providing enhanced juvenile rearing opportunities by pond construction.

of 63

The project design and resource protection measures would minimize or prevent adverse effects on

aquatic species (including anadromous salmonids) and their habitat at the site scale and render

discountable effects on these species downstream at the 7th- and 5th-field watershed scales. A trend

towards listing under the ESA is not anticipated, and viability is not at risk relative to the project because

short-term effects on aquatic habitat would be neutral, the project meets Standards and Guidelines, and

the project would be expected to positively affect anadromous fish rearing and migration habitat in the

long term.

IX. Project Elements and Effects Summary

Direct Effects to species: No direct adverse effects (see page 26).

Indirect Effects: Increased sediment delivery to anadromous fish bearing stream-reaches is the

greatest threat to fish and/or their habitat. This threat comes from the removal of groundcover

and the removal of large boulders and cobble associated with creating the new pond and

removing the boulder cascade at the mouth of O’Neil Creek. Project design and controls reduce

the risk of adverse impacts from these activities such that all habitat Indicators are maintained

with no significant effects at the 7th

, and 5th

field watershed scales. Key components of the

controls are Project design features and BMPs ensuring that sediment and flow are either

prevented from or minimized to insignificant amounts when enteringchannels. Monitoring of

BMP on the KNF has shown a high degree of implementation and effectiveness. Further, long-

term benefits to Riparian Reserves are provided by the Project through planting of native riparian

vegetation and reseeding of all areas disturbed during project activities.

ELEMENT SUMMARY: as supported by rationale provided in Section V.

The Project Element considered for analyses is habitat restoration (creating additional pond

habitat and removing a partial passage barrier), riparian planting, and water drafting (for

watering plants after they are planted for up to two years following project completion)

• Habitat Restoration – creating additional pond habitat and removing a partial passage

barrier

Creating additional pond habitat, banks around the pond, and the shallow bench around the

shoreline of the pond will have insignificant negative effects on Suspended Sediment and

Substrate Character and Riparian Reserves and neutral effects to all other indicators.

Removal of the partial passage barrier will have insignificant negative effects on Suspended

Sediment and Substrate Character and Riparian Reserves and neutral effects to all other

indicators.

• Riparian Planting and reseeding

Planting of riparian vegetation and reseeding all areas disturbed by heavy equipment during

project activities will have a neutral short term effect and a long term positive effect on

Suspended Sediment and Substrate Character and Riparian Reserves and neutral effects to all

other indicators.

• Water Drafting

Neutral effects to all indicators.

of 63

• Fish Blocking Nets and Silt Fencing

Neutral effects to all indicators.

of 63

Table 6. Summary of the effects on SONCC Coho salmon CH, SONCC Coho salmon and UKT Chinook

salmon EFH and KMP steelhead trout habitat of the O’Neil Creek Pond Project for Project

Element/Indicator combinations.

Indicators

Pond

Construction

and Barrier

Modification

Riparian

Planting

and

reseeding

Silt Fencing

and Fish

Blocknets

Water

Drafting Reason for No Effect

Temp. 0 0 0 0

No change in stream shading

Turbidity

-+ 0 -+ 0

There will be only two brief

localized episodes (few

minutes to a few hours) of

elevated turbidity that will

affect about 30 feet of lower

O,Neil Creek and the

Klamath River at the O’Neil

Creek confluence

Chemical

Contamination 0 0 0 0

No chemical treatments will

be used

Nutrients

0 0 0 0

PDFs and BMPs are applied

and based on field review

and low intensity of the

action

Physical Barriers 0 0 0 0

No barriers removed or

constructed

Substrate

-+ 0 -+ 0




action will result in

Insignificant Negative effects

and a long term positive

effects to SONCC Coho

salmon CH, and KMP

steelhead trout habitat and

Insignificant Negative effects

to UKT Chinook salmon and

coho salmon EFH.

Large Woody

Debris 0 0 0 0

No removal of woody debris

within RRs

Pool Frequency

and Quality 0 0 0 0

No change in peak flows

Off-Channel

Habitat 0 0 0 0

Not present in the section of

O’Neil Creek associated with

the Project

Refugia 0 0 0 0

Water temperature is not

affected

Width/Depth

Ratio 0 0 0 0

No sediment delivery will

result

Streambank

Condition 0 0 0 0

No sediment delivery will

result

Floodplain 0 0 0 0 No change in flows or

of 63

Connectivity sediment delivery

Change in

Peak/Base Flows 0 0 0 0

No significant increase in

ERA (USDA Forest Service

2011a)

Increase in

Drainage

Network

0 0 0 0

No new system roads will be

constructed

Road Density

and Location 0 0 0 0

No new system roads will be

constructed

Disturbance

History 0, + 0 0 0




action Riparian

Reserves -, + 0 0 0

- = Insignificant negative effects to SONCC Coho salmon CH, UKT Chinook salmon and coho salmon EFH,

and KMP steelhead trout habitat

0 = Neutral effects

+ = Positive effects

-/+ = Insignificant negative effects and insignificant positive effects

-* = More than insignificant negative effects

The following conclusions, with consideration of the effects from Project Elements to habitat

Indicators, lead to my final determination of effects that the proposed project will have on

SONCC coho salmon, CH, UKT Chinook salmon, EFH, and KMP steelhead trout and its habitat:

1) There will be no changes to the functional level of fish habitat Indicators.

2) Spawning and rearing habitat quality and quantity will be negligibly adversely affected in the

short-term only.

3) Migration and rearing habitat will be improved in the long-term.

4) The will be only two brief and minor episodes of adverse effects to water quality: (1) during

implementation in summer there will be a few minutes to a few hours of elevated turbidity in

approximately 30 feet of lower O’Neil Creek and in the thermal refugia at the confluence of

O’Neil Creek and the Klamath River, and (2) in the first high flow in the wet season

following implementation turbidity may be elevated in the lower 30 feet of O’Neil Creek and

in the Klamath River confluence for a few minutes to a few hours as the channel re-adjusts in

response to the large boulder no longer being in place.

5) Project Design Features, including BMPs (see Appendix B for complete list of project

BMPs) will be implemented to minimize or eliminate effects of the proposed project to

anadromous fish and their habitat in the short and long term at the site and watershed scales.

6) Wet Weather Operation Standards will be used to guide operations during periods of wet

weather.

7) Less than 0.05% of the 5th

field watershed analysis area will be disturbed by Project

activities. Less than 0.5% of the 7th

field watersheds analysis areas will be disturbed by

Project activities.

8) There is negligible risk of adverse direct effects to coho salmon

of 63

PROJECT EFFECTS DETERMINATION KEY FOR SPECIES AND DESIGNATED CRITICAL HABITAT

1) Do any of the Indicator summaries have a positive (+) or negative (-) conclusion?

Yes – Go to 2

No – No Effect

2) Are the Indicator summary results only positive?

Yes – NLAA

No – Go to 3

3) If any of the Indicator summary results are negative, are the effects insignificant or discountable?

Yes – NLAA

No – LAA, fill out Adverse Effects Form

X. ESA Effects Determination: It is my determination that the O’Neil Creek Pond Project May Affect but Not Likely to

Adversely Affect SONCC coho salmon or their CH.

XI. Sensitive Species Effects Determination It is my determination that the O’Neil Creek Pond Project will not result in a trend toward listing

or loss of viability of KMP steelhead trout or UKT Chinook salmon.

XII. EFH Assessment KNF stream surveys, California Department of fish and Game information and professional

judgment of fisheries biologists has been compiled into the KNF steelhead trout distribution

layer in the KNF Geographic Information Systems electronic library. The use of the KNF

steelhead trout distribution to define SONCC coho salmon and Upper Klamath-Trinity

River(UKTR) spring and fall-run Chinook salmon EFH is a conservative estimate of the

distribution of SONCC coho salmon and UKTR Chinook salmon because their distribution is

likely somewhat less extensive than steelhead trout due to differences in swimming and jumping

abilities. Steelhead trout are typically found farther upstream than coho and Chinook salmon.

The project area includes approximately 0.012 mile of habitat in the O’Neil Creek watershed,

and has the potential to influence anadromous habitat for some distance downstream. It is

assumed that SONCC coho salmon and KMP steelhead trout inhabit O’Neil Creek within the

project area and that all three species inhabit the Klamath River within and downstream of the

project area. Table 4 indicates the approximate distance between PEs and Chinook salmon, CH

for coho salmon and steelhead trout (which is equivalent to EFH). This evaluation considered the

lower 0.012 mile of O’Neil Creek as habitat for SONCC coho salmon and KMP steelhead trout

and the section of the Klamath River from the confluence with O’Neil Creek extending

approximately 0.75 miles downstream to the confluence with Louie Creek from the confluence

with Salt Gulch, as habitat for all three species.

of 63

The KNF used their steelhead distribution map for the Analysis Area as the basis to delineate the

extent of coho salmon CH, and thus Chinook salmon and coho salmon EFH. The effects

analysis in Chapter VI considers effects to Pacific salmonid habitat in general, and since habitat

requirements for coho salmon and Chinook salmon are similar, the effects of the Project as

described in Chapter VI for coho salmon CH are identical for EFH.

Therefore, it is my determination that the O’Neil Creek Pond Project may adversely affect coho

salmon and Chinook salmon EFH.

of 63

Literature Cited

Barnhart, R.A. 1986. Species profiles: Life histories and environmental requirements of

coastal fishes and invertebrates (Pacific Southwest)--steelhead. U.S. Fish and Wildl. Serv. Biol.

Rep. 82(11.60). 21 pages.

Bell, M.C. 1986. Fisheries Handbook of Engineering Requirements and Biological Criteria.

US Army Corp of Engineers, Office of the Chief of Engineers, Fish Passage Development and

Evaluation Program, Portland, Oregon.

Burgner, R.L., J.T. Light, L. Margolis, T. Okazaki, A. Tautz, and S. Ito. 1992. Distribution

and origins of steelhead trout (Oncorhynchus mykiss) in offshore waters of the North Pacific

Ocean. Int. North Pac. Fish Comm. Bull. 51. 92 pages. In Busby et al. (1996).

Busby, P. J., Wainwright, T. C., Bryant, G. J., Lierheimer, L. J., Waples, R. S., Waknitz, F.

W., and Lagomarsino, I. V. 1996. Status review for Klamath Mountains Province steelhead.

NOAA technical memorandum NMFS-NWFSC-19.

Hassler, T.J. 1987. Species profiles: Life histories and environmental requirements of coastal

fishes and invertebrates (Pacific Southwest)--coho salmon. U.S. Fish and Wildl. Serv. Biol. Rep.

82(11.70). 19 pages

Healey, M.C. 1991. The life history of Chinook salmon (Oncorhynchus tshawytscha). Pages

213-393 In: C. Groot and L. Margolis (eds.), Life history of Pacific salmon. Univ. B.C. Press,

Vancouver, B.C.

Knechtle, M. 2011. Shasta River River Counting Weir cumulative data. CA Dept of Fish

and Game. December

Meehan, W.R., ed. 1991. Influences of forest and rangeland management on salmonid fishes

and their habitats. American Fisheries Society Special Publication 19.

Meyers, J.M., R.G. Kope, G.J. Bryant, D. Teel, L.J. Lierheimer, T.C. Wainwright, W.S.

Grand, F.W. Waknitz, K. Neely, S.T. Lindley, and R.S. Waples. 1998.

Status review of chinook salmon from Washington, Idaho, Oregon, and California. U.S. Dept.

Commer., NOAA Tech. Memo. NMFS-NWFSC-35, 443 p.

www.nwfsc.noaa.gov/publications/techmemos/tm35/chapters/07disconesu.htm#ktr

Nickelson, T.E., J.W. Nicholas, A.M. McGie, R.B. Lindsay, D.L. Bottom, R.J. Kaiser, and

S.E. Jacobs. 1992. Status of anadromous salmonids in Oregon coastal basins. Unpublished.

Reeves, G.H., F.H. Everest, and J.D. Hall. 1987. Interactions between the redside shiner

(Richardsonius balteatus) and the steelhead trout (Salmo gairdneri) in western Oregon: the

influence of water temperature. Can. J. Fish. Aquat. Sci. 44:1603-1613.

Rich, A.A. 1997. Testimony of Alice A. Rich, Ph.D., regarding water rights applications for the

Delta Wetlands Project, proposed by Delta Wetlands Properties for Water Storage on Webb

Tract, Bacon Island, Bouldin Island, and Holland Tract in Contra Costa and San Joaquin

of 63

Counties. July. Calif. Dept. of Fish and Game Exhibit DFG-7. Submitted to State Water

Resources Control Board.

Sandercock, F.K. 1991. Life history of coho salmon. Pages 397-445 In C. Groot and L.

Margolis (eds.), Pacific salmon life histories. Univ. British Columbia Press, Vancouver. 564

pages.

USDA Forest Service, US Department of Commerce-NMFS, US Department of the

Interior-USFWS and BLM (USDA-USDC-USDI). 2004. Analytical Process for Developing

Biological Assessments for Federal Actions Affecting Fish Within the Northwest Forest Plan

Area.

USDA Forest Service. 2011. Fishery Resource Report, O’Neil Pond Project. 2011.

USDA Forest Service. 2011a. Geology/Hydrology Report, O’Neil Pond Project 2011.

USDA Forest Service. 2002. Field Guide for Use with Wet Weather Operation Standards

(WWOs). Klamath National Forest.

USDA Forest Service. 2000. Water Quality Management for Forest system Lands in California,

USDA Forest Service. Pacific Southwest Region.

USDA Forest Service. 1998. Pacific Southwest Region Sensitive Species List. June.

USDA Forest Service. 1995. Record of Decision for the Final Environmental Impacts

Statement for the Klamath National Forest and Land and Resource Management Plan. Klamath

National Forest. (LRMP) pg. 3- 12.

USDA Forest Service. 1991. Forest Service Manual 2672.42.

USDI NMFS. 2001. Water-Drafting Specifications. NMFS Southwest Region.

USDI NMFS. 1996. Making Endangered Species Act Determinations of Effects for Individual

or Grouped Actions at the Watershed Scale. NMFS Environmental and Technical Services

Division, Habitat Conservation Branch. August (included as Attachment 3 in the 1997 Biological

Opinion for the KNF LRMP).

Weitkamp, L.A., T.C. Wainwright, G.J. Bryant, G.B. Milner, D.J. Teel, R.G. Kope, and

R.S. Waples. 1995. Status review of coho salmon from Washington, Oregon, and California.

U.S. Dep. Commer., NOAA Tech Memo. NMFS-NWFSC-24, Northwest Fisheries Science

Center, Seattle, Washington. 258 pages.

of 63

APPENDIX A: Project Map

See next pages

of 63

Appendix B. Applicable Best Management Practices

Best Management Practices (BMPs) were developed to comply with Section 208 of the Clean Water Act.

BMPs have been certified by the State Water Quality Resources Control Board and approved by the

Environmental Protection Agency (EPA) as a way of protecting water quality from impacts stemming

from non-point sources of pollution. These practices have been applied to forest activities and have been

found to be effective in protecting water quality within the Klamath National Forest. Specifically,

effective application of the R-5 USDA Forest Service BMPs has been found to maintain water quality that

is in conformance with the Water Quality Objectives in the North Coast Region Water Quality Control

Board’s (NCRWQCB) Basin Plan.

The following list of BMPs will be implemented in the O’Neil Creek Pond Project. A description of the

objective of each BMP is included, as well as how each practice will be specifically implemented within

the project. For additional information on the BMPs and their objectives, see Water Quality Management

for Forest System Lands in California (USDA Forest Service 2000).

BMP 2-2 (Erosion Control Plan): This BMP limits and mitigates erosion and

sedimentation through effective planning prior to initiation of construction activities and

through effect contract administration during construction.

• Silt fencing will be placed at the inlet of the proposed pond to minimize any potential suspended

sediment from entering any flowing water in O’Neil Creek or the Klamath River.

• Following construction, all disturbed areas will be stabilized and reseeded with a native grass



meadow barley (Hordeum brachyantherum), pine bluegrass (Poa secunda), Spanish clover (Lotus

purshianus), three week fescue (Vulpia microstachys), and tufted hairgrass (Deschampsia

of 63

cespitosa).

BMP 2-3 (Timing of Construction Activities): This BMP is used to minimize erosion by conducting

operations during minimal runoff periods.

• Work will take place during the summer-early fall low flow, when the proposed pond area is dry,

and disconnected from all adjacent wetted channels.

• Wet Weather Operation Standards will be used to guide operations, during periods of wet

weather. Earth scientists will examine field conditions to determine when the soil and/or access

road have dried out enough to enable operations to resume without risk of watershed impacts.

BMP 2-12 (Servicing and Refueling of Equipment): To prevent pollutants such as fuels, lubricants,

bitumens and other harmful materials from being discharged into or near rivers, streams, and

impoundments, or into natural or man-made channels.

• Equipment will not be refueled or serviced on the Klamath River floodplain or within 200 feet of

a stream channel.

• Equipment in poor repair (particularly oil leaks and/or cracked old hydraulic lines) will not be

allowed to operate in this project.

• A Spill Prevention, Containment and Counter-Measures Plan is required for this project. In the

plan, contractors and sub-contractors will be required to take all reasonable precautions to prevent

pollution of air, soil, and water. Contractors and/or sub-contractors shall furnish oil absorbing

mats for use under all temporarily stationary equipment on the Klamath River floodplain or

within 200 feet of a stream channel. Contractors and/or sub-contractors shall furnish oil

absorbing mats for use under all equipment that must be serviced (because of mechanical

problems) on the Klamath River floodplain or within 200 feet of a stream channel. Contractors

and/or sub-contractors shall keep oil absorbing mats and pads on site in sufficient supply to

absorb potential contaminates from active leaks and to soak up excess surface contaminates from

the ground in the event of a spill.

BMP 2-13 (Control of Construction and Maintanance Activities Adjacent to SMZs): To protect

water quality by controlling construction and maintenance actions within and adjacent to any streamside

management zone so that the following SMZ functions are not impaired.

• Silt fencing will be placed to allow little/no suspended sediment to enter any running water in

O’Neil Creek or the Klamath River

• Work will take place during the summer-early fall low flow, when the proposed pond area is dry

and disconnected from adjacent wetted channels.

• Wet Weather Operation Standards will be used to guide operations, during periods of wet

weather. Earth scientists will examine field conditions to determine when the soil and/or access

road have dried out enough to enable operations to resume without risk of watershed impacts.

• Spoils (boulders) from the excavation will be placed in linear rows along the edges of created

wetland habitat to improve the potential for these habitats to persist through large flood events.






cespitosa).

• Approximately 350 local native willow (Salix spp.), white alder (Alnus rhombifolia) and black



of 63

apart along the toe of each stream bank and extend upslope approximately 10 feet (3 rows).

Local willow species may include, but are not limited to red willow (Salix laevigata), Pacific

willow (Salix lucida ssp. lasiandra), and narrow leaf (Salix exigua).

BMP 2-14 (Controlling In-Channel Excavation): To minimize stream channel disturbances and related

sediment production.



• Work will take place during the summer low flow, when the proposed pond area is dry, and

disconnected from adjacent wetted channels.

• Spoils (boulders) from the excavation will be placed in linear rows along

the edges of the created wetland habitat to improve the potential for created habitats

to persist after large flood events (50-100 yr).






cespitosa).







BMP 7.1 – Watershed Restoration: To repair watershed conditions and improve water quality and soil

stability.

• A 70,000 lb excavator will be used to construct additional pool habitat on the O’Neil Creek

alluvial delta/Klamath River Floodplain at the mouth of O’Neil Creek. This will be done by

excavating large boulders from the floodplain of the Klamath River to extend, widen and deepen

pond habitat connected to the alluvial delta at the mouth of O’Neil Creek. The pond will be

excavated to a depth as great as 6 feet. A shallow bench, approximately one foot in depth, will

also be excavated around the perimeter and along the northern portion of the proposed pond to

create shallow water habitat and encourage growth of hydrophytic vegetation.

• Several large boulders will be left within the proposed pond to provide complexity and cover.

Spoils (mainly boulders and cobble) from the excavation will be placed in linear rows along the

edges of the created wetland habitat to improve the potential for created habitats to persist after

large flood events (50-100 yr). The excavator will also be used to remove a boulder or boulder

cascade at the mouth of O’Neil Creek that currently impedes salmonid access to O’Neil Creek

during low flows during the warm summer months.






cespitosa).



of 63





BMP 7.2 – Conduct Floodplain Hazard Analysis and Evaluation: To avoid, where possible, the long

and short-term adverse impacts to water quality associated with the occupancy and modification of

floodplains.

• Work will take place during the summer low flow, when the proposed pond area is dry and

disconnected from adjacent wetted channels.



• Fish block nets will be installed to keep fish from entering area being worked on by the

excavator.






cespitosa).





Riparian Reserves

One site potential tree height as per Forest standards in the Project area is 150 feet on each side

of a qualifying stream channel. Since Northwest Forest Plan ROD-defined standard slope

distance for riparian reserve widths of two site potential tree heights or 300 feet for anadromous

and resident fish bearing streams (whichever is greater) and one site potential tree height or 150

feet for non fish-bearing streams (whichever is greater), the riparian reserve width of 300 feet for

fish-bearing streams and 150 feet on each side of an active stream channel for non fish-bearing

streams will be used. Project activities will occur within the designated O’Neil Creek and

Klamath River Riparian Reserve area. Based on setbacks from wetted channels, lack of fine-

textured sediment in the Project action area, and Project design features, impact to effective

canopy shade are expected to be insignificantly small, while impacts to other constituent

elements associated with SONCC coho salmon CH are expected to be discountable.

Wet Weather Operation Standards

Wet Weather Operation Standards (WWOS; USDA Forest Service 2002) will be used to guide

operations during periods of wet weather. Earth scientists will examine field conditions to

determine when the soil and/or road have dried out enough to enable operations to resume

without risk of watershed impacts. These standards apply to the access road, for the pond

construction and boulder cascade areas are devoid of fine-textured sediment.

of 63

APPENDIX C

Klamath National Forest Matrix: Table of Population and Habitat Indicators for Use on the Klamath National Forest in the Northwest Forest Plan Area

Aquatic Habitat Conditions Analysis Guidelines

The table below shows criteria used to determine baseline conditions in 7th-and 5th-field watersheds within the KNF boundaries. The

existing conditions and effects on Indicators are discussed in the narrative within the BA/BE and are summarized in the table/checklist

format. The table below represents the most recent Level 1 review as completed by J. Perrochet (KNF) and D. Flickinger (NMFS) in

April 2007.

Klamath National Forest Tributaries Table of Pathways and Indicators:

Pathways Indicators Properly Functioning At Risk Not Properly Functioning

Habitat: Non Watershed Condition Indicators

Water Quality: Temperature (1)

1st - 3rd Order

Streams

[instantaneous]

69°For less > 69 to 70.5°F > 70.5°F

4th

–5th Order

Streams

[7 Day

Maximum]

70.5°F or less ~ 21.4°C > 70.5 to 73.5°F > 73.5°F; ~23°C

Suspended

Sediment/

Turbidity (2)

Low Medium High

Compliance with Clean Water Act requirements for suspended sediment and turbidity at the site and project scale is

achieved through application of appropriate Best Management Practices and other measures as specified by permits from

relevant State Water Quality Control Board.

Chemical/

Nutrient

Contamination (3)

Low levels of contamination from

agriculture, industrial, and other

sources; no excess nutrients. No CWA

303d designated reaches.

Moderate levels of contamination from


sources; some excess nutrients. One

CWA 303d designated reach.

High levels of contamination from


sources; high levels of nutrients. More

than one CWA 303d designated reach.

Habitat

Access:

Physical Barriers

(3)

Any man-made barriers present in

watershed allow upstream and

downstream passage at all flows.

One or more human -made barriers

present in watershed do not allow

upstream and/or downstream passage at

Human-made barriers present in

watershed do not allow upstream and/or

downstream passage at a range of flows

of 63



base/low flows. for at least one life history stage.

Habitat

Elements:

Substrate

character (4)

Use USLE and GEO model to determine functioning level and potential effects of sediment delivery to streams that may

affect anadromous fish and their habitat. Existing condition for fines and embeddedness can also be used.

Less than 15% fines (<2 mm) in

spawning habitat (pool tail-outs, low

gradient riffles, and glides) and cobble

embeddedness less than 20%.

15% or greater fines (<2 mm) in


gradient riffles, and glides) and/or

cobble embeddedness is 20% or

greater.

Greater than 20% fines (<2 mm) in


gradient riffles, and glides) and cobble

embeddedness greater than 25%.

Large Woody

Debris (3)

More than 20 pieces of large wood

(>24 inches in diameter and >50 feet in

length) per mile; also adequate source

of woody debris are available for both

long- and short-term recruitment.

Current levels are being maintained at

minimum levels desired for “properly

functioning” but potential sources for

long term woody debris recruitment are

lacking to maintain these minimum

values.

Current levels are not at those desired

levels for “properly functioning” and

potential sources of woody debris for

short and/or long term recruitment are

lacking.

Pool Quality

(Pool = 1meter

deep) and

Frequency (4)

At least 1 pool every 3 to 7 bankfull

channel widths. These pools should

occupy at least 50% of the low-flow

channel width and all have a maximum

depth of at least 36 inches.

At least 1 pool every 3 to 7 bankfull

channel widths. These pools should

occupy at least 50% of the low-flow

channel width. At least half of the pools

have a maximum depth of at least 36

inches.

Less than 1 pool every 7 bankfull

channel widths and/or less than half of

the pools have a maximum depth of at

least 36 inches.

Off-channel

Habitat (3)

Watershed has many ponds, oxbows,

backwaters and other off channel areas

with cover; and side channels are low

energy areas.

Watershed has some ponds, oxbows,

backwaters and other off channel areas

with cover; but side channels are

generally high energy areas.

Watershed has few or no ponds,

oxbows, backwaters or other off-

channel areas.

Refugia

(important

remnant habitat

for sensitive

aquatic species)

(3)

Habitat capable of supporting strong

and significant populations are

protected (e.g., by intact riparian

reserves or conservation areas, ground

water upwelling areas and seeps); and

are well distributed and connected for

all life stages and forms of the species.

Habitat capable of supporting strong

and significant populations are

insufficient in size, number, and

connectivity to maintain all life stages

and forms of the species

Adequate habitat refugia do not exist.

of 63



Channel

Condition and

Dynamics:

Width/Depth

Ratio (5)

Width-to-Depth ratio <12 on all reaches

that could otherwise best be described

as 'A', 'G', and 'E' channel types. Width-

to-Depth ratio >12 on all reaches that

could otherwise best be described as

'B', 'F', and 'C' channel types. No

braided streams formed due to

excessive sediment loads

More than 10% of the reaches are

outside of the ranges given for

Width/Depth ratios for the channel

types specified in “Properly

Functioning” block. Braiding has

occurred in some alluvial reaches as a

result of excessive aggradation due to

high sediment loads.

More than 25% of the reaches are

outside of the ranges given for

Width/Depth ratios for the channel

types specified in “Properly

Functioning” block. Braiding has

occurred in many alluvial reaches as a

result of excessive aggradation due to

high sediment loads

Streambank

Condition (3)

>80% of any stream reach has >90%

stability

50–80% of any stream reach has >90%

stability

<50% of any stream reach has >90%

stability

Flow /

Hydrology:

Floodplain

Connectivity (3)

Off-channel areas are frequently

hydrologically linked to main channel;

overbank flows occur and maintain

wetland functions, riparian vegetation,

and succession.

Reduced linkage of wetland,

floodplains, and riparian areas to main

channel; overbank flows are reduced

relative to historic frequency, as

evidenced by moderate degradation of

wetland function, riparian

vegetation/succession.

Severe reduction in hydrologic

connectivity between off-channel,

wetland, floodplain, and riparian areas;

wetland area drastically reduced and

riparian vegetation/succession altered

significantly.

Increase in

Drainage

Network (3)

Zero or minimum increases in active

channel length correlated with human

caused disturbance (e.g., trails, ditches,

compaction, impervious surface, etc).

Low to Moderate increases in active

channel length correlated with human

caused disturbance (e.g., trails ditches,

compaction, impervious surface, etc).

Greater than moderate increase in

active channel length correlated with

human caused disturbance (e.g., trails

ditches, compaction, impervious

surface, etc).

Watershed Condition Indicators

Watershed

Conditions:

Road Density and

Location (3)

Less than 2 miles per square mile. Two to three miles per square mile. Over 3 miles per square mile.

Disturbance

History (7)

CWE model indicator values (USLE,

Mass-Wasting, and ERA) are not above

1.0. Clarify and verify conditions and

risk through field reviews and/or other

available info, as available.

One or two of the CWE model

indicator values are above threshold of

1.0. Clarify and verify conditions and

risk through field reviews and/or other


Three of the CWE model indicator

values are above threshold of 1.0.

Clarify and verify conditions and risk

through field reviews and/or other


Riparian Reserves The riparian reserve system provides Moderate loss of connectivity or Riparian reserve system is fragmented,

of 63



– NW Forest Plan

(3)

adequate shade, large woody debris

recruitment, and habitat protection and

connectivity in all sub watersheds, and

buffers or includes known refugia for

sensitive aquatic species (> 80% intact),

and/or for grazing impacts; percent

similarity of riparian vegetation to the

potential natural

community/composition > 50%.

function (shade, LWD recruitment, etc)

of riparian reserve system, or

incomplete protection of habitat and

refugia for sensitive aquatic species

(approx. 70–80% intact), and/or for

grazing impacts; percent similarity of

riparian vegetation to the potential

natural community/composition 25–

50% or better.

poorly connected, or provides

inadequate protection of habitat and

refugia for sensitive aquatic species

(approx. less than 70% intact), and/or

for grazing impacts; percent similarity

of riparian vegetation to the potential

natural community/composition is 25%

or less.

Disturbance

Regime (7)

Environmental Disturbance is short

lived; predictable hydrograph, high

quality habitat and watershed

complexity providing refuge and

rearing space for all life stages or

multiple life-history forms. Natural

processes are stable. This is best

quantified through the CWE modeling

described for Disturbance History.

Scour events, debris torrents or

catastrophic fire are localized events

that occur in several minor parts of the

watershed. Resiliency of habitat to

recover from environmental

disturbances is moderate. This is best


described for Disturbance History

Frequent flood or drought producing

highly variable and unpredictable

flows, scour events, or high probability

of catastrophic fire exists throughout a

major part of the watershed. The

channel is simplified, providing little

hydraulic complexity in the form of

pools or side channels. Natural

processes are unstable. This is best


described for Disturbance History

Summary Integration

of all species and

habitat indicators

How do the effects to indicators affect each fish species and their habitat? Describe by species and by 7th

and 5th

field watersheds. See

AP guidance. In addition to the narrative summary, use Summary Table.

of 63

Footnotes to Table Above: Table of Population and Habitat Indicators for Use on the Klamath National Forest in the Northwest Forest

Plan Area, as adjusted from Appendix A in the Analytical Process.

The table, as designed in the 2004 Analytical Process, and in earlier versions (1997 NMFS BO for the LRMP), suggests values to

determine a level of functioning for anadromous fish bearing streams. A note about rigid values to assess level of functioning: In

addition to fixed habitat parameters not allowing for natural variability, they set standards that may be geomorphically inappropriate

(Bisson et al. 1997). Variability is an inherent property of aquatic ecosystems in the Pacific Northwest and habitats at any given

location will change from year to year, decade to decade, and century to century (Bisson et al. 1997). Healthy lotic ecosystems require

different parts of the channel system to exhibit very different in-channel conditions and that those conditions change through time

(Reid and Furniss 1998). Therefore, a conclusion of function must be evaluated with professional judgment recognizing the streams

capability to perform within rigid values. In some cases, a stream’s morphology, aspect, or size may not support “Properly

Functioning” criteria values for one or more habitat Indicators. If an Indicator for a particular stream is determined to be functioning at

its capability (due to morphology, aspect, or size), it is rated as Properly Functioning even if it doesn’t meet Appendix A table criteria

values. The table serves to identify values to determine the quality of baseline conditions; the Checklists (Appendix B) serve to

summarize the baseline conditions and effects by watershed.

(1) Proper Functioning criteria for 4th–5th Order streams is derived from temperature monitoring near the mouth of streams

considered to be pristine or nearly pristine (Clear, Dillon, and Wooley Creeks – seven-day maximum temperatures as high as

70.5°F have been recorded on these streams [EA Engineering, 1998 Salmon River and Dillon Creek Watershed Fish Habitat and

Channel Type Analysis, Appendix 2]). At-Risk criteria for 4th–5th order streams is derived from monitoring in streams that

support populations of anadromous fish, although temperatures in this range (70.5°F to 73.5°F) are considered sub-optimal. A Not

Properly Functioning criterion is sustained temperatures above 73.5°F that cause cessation of growth and approach lethal

temperatures for salmon and steelhead. Properly Functioning criteria for 1st–3rd order streams is derived from Desired Future

Conditions values given in the environmental impact statement for the KNF LRMP, page 3-68. At Risk and Not Properly

Functioning are assigned on a temperature continuum with values given for 4th–5th order streams, with the maximum

instantaneous temperature of At Risk of 1st–3rd order streams coinciding with the minimum 7-day maximum of 4th–5th order At

Risk streams.

(2) Turbidity: NTU data for streams in the Klamath River system on the Klamath National Forest are not available. Professional

judgment on how fast a stream clears after a peak flow, stream surveys data for substrate conditions, and/or the CWE modeling are

used to estimate the existing condition and post-action condition for this Indicator. The Analytical Process Table suggests using

fine sediment as a surrogate. The risk of sediment delivery to streams is evaluated through the CWE modeling as described below

in (4). Also, compliance with Clean Water Act requirements for suspended sediment and turbidity at the site and project scale is

achieved through application of appropriate Best Management Practices and other measures as specified by permits from relevant

State Water Quality Control Board.

1. Properly Functioning: Water clarity returns quickly (within several days) following peak flows (“Low”).

of 63

2. At Risk: Water clarity slow to return following peak flows (“Medium”).

3. Not Properly Functioning: Water clarity poor for long periods of time following peak flows. Some suspended sediments occur

even at low flows or base flow (“High”).

(3) Criteria unchanged from Analytical Process Table. Include consideration of whether the project is in a Key Watershed, as Key

Watershed were develop to serve as ‘anchors’ for aquatic dependent species.

(4) Properly Functioning criteria for percent fines in gravel is taken from environmental impact statement for the KNF LRMP

(page 3-68) can also be used to assess existing conditions when that information is available. When that information is

unavailable, professional judgment is used to describe existing conditions and to estimate effects based upon model output

interpretation, research results, or other information. The KNF CWE modeling procedure (Appendix G) describes the risk

(probability) of Project-caused sediment production. For Existing and Post Action:

1. Properly Functioning: USLE and GEO values are less than 1.0.

2. At Risk: USLE and GEO values are between 1.0–1.20.

3. Not Properly Functioning: USLE and GEO values are greater than 1.20.

(5) The Width-to-Depth ratio for various channel types is based on delineative criteria of Rosgen (1996). Properly Functioning

means that Width-to-Depth ratio falls within expected channel type as determined by the other four delineative factors

(entrenchment, sinuosity, slope, and substrate). Aggradation on alluvial flats causing braiding is well known phenomenon that

often accompanies changes in Width-to-Depth ratio as watershed condition deteriorates. Stream width is a function of streamflow

occurrence and magnitude, size and type of transported sediment, and the bed and bank materials of the channel (Rosgen 1996).

Channel widths generally increase downstream as the square root of discharge. Channel widths can be modified by changes in

riparian vegetation, changes in streamflow regimes, and changes in sediment supply. Mean depth of channels varies greatly by

reach under different discharges due to the sequence of riffle and pool bed features. Width-to-Depth ratios vary with the

dimensions of the channel cross section for a given slope, boundary roughness as a function of streamflow and sediment regime,

bank erodibility, degree of entrenchment and the distribution of energy in the stream channel (Rosgen 1996). The table in indicates

that confined or entrenched channel types (such as A, G, and E types) are Properly Functioning when Width-to-Depth ratios are

less than 12, and wider channel types (such as B, C, and F types) are Properly Functioning when Width-to-Depth ratios are greater

than 12. To meet the Properly Functioning criteria channels must also have no or minimal braiding due to excessive sediment.

(6) The table values in the 2004 Analytical Process suggest using hydrograph information to estimate existing flow conditions and

post-project changes in flow. Hydrograph information is not available for most watersheds on the Forest. Forest Service Region 5

uses ERA/TOC to determine the existing risk as well as the risk of adverse effects to flows (Appendix G).

(7) The three components of the KNF CWE model are used to determine conditions and risk to this Indicator (Appendix G). The

KNF CWE model components replace the use of ECA because ECA is not used in Forest Service Region 5. Agreed to by Yip and

Perrochet (Level 1) April 8, 2003.

1. Properly Functioning: All three model values (USLE, GEO and ERA) are less than 1.0 risk ratio; that is, below threshold.

of 63

2. At Risk: One or two model values is 1.0 or greater; that is, at or exceeding threshold.

3. Not Properly Functioning: Values for all three models is greater than 1.0.

of 63

APPENDIX D Tables/Checklists for Documenting the Environmental Baseline

and Effects of Project(s) on Relevant Indicators for the Project

Diagnostic or Pathway:

Indicators

Existing Conditions

O’Neil Creek 7th-

field subwatershed

Effects of the Action(s)

O’Neil Creek 7th-

field subwatershed

Properly

Functioning At Risk

Not

Properly

Functioning Restore Maintain Degrade

Water Quality

Temperature

WA 1999 X

Sediment-Turbidity WA 1999 X

Chemical Contamination PJ X

Habitat Access

Physical Barrier

WA 1999 X

Habitat Elements

Sediment-Substrate

WA 1999 X

LWD WA 1999 X

Pool Frequency WA 1999 X

Pool Quality WA 1999 X

Off-channel Habitat NA NA NA NA

Refugia WA 1999 X

Channel Cond & Dyn

W/D Ratio

WA 1999 X

Streambank Cond. WA 1999 X

Floodplain Cond. WA 1999

Flow /Hydrology

Peak/Base Flow

WA 1999 X

Drainage Net Incrs WA 1999 X

Watershed Cond.

Road Dens/Loc

WA 1999 X

Disturbance History and

Regime

WA 1999 X

Riparian Reserves WA 1999 X

PJ: Professional Judgment

WA 1999: Thompson/Seiad/Grider Ecosystem Analysis (1999)

N/A: Not Applicable

of 63


Indicators

Existing Conditions

Bittenbender Creek-Klamath River 6th

-

field subwatershed


Bittenbender Creek-Klamath River

6th

-field subwatershed

Properly

Functioning At Risk

Not

Properly


Water Quality

Temperature

WA 1999 X



Habitat Access

Physical Barrier

PJ X

Habitat Elements

Sediment-Substrate

WA 1999 X

LWD WA 1999 X




Refugia PJ X

Channel Cond & Dyn

W/D Ratio

WA 1999

PJ

X

Streambank Cond. WA 1999

PJ

X


PJ

X

Flow /Hydrology

Peak/Base Flow

WA 1999 X


Watershed Cond.

Road Dens/Loc

WA 1999 X


Regime

WA 1999 X

Riparian Reserves PJ* WA 1999 X



N/A: Not Applicable

* Considered Properly Functioning on federal land and At Risk on private land

of 63


Indicators

Existing Conditions

Seiad Creek-Klamath River 5th

-field

watershed


Seiad Creek-Klamath River 5th

-

field watershed

Properly

Functioning At Risk

Not

Properly


Water Quality

Temperature

WA 1999 X



Habitat Access

Physical Barrier

PJ X

Habitat Elements

Sediment-Substrate

WA 1999 X

LWD WA 1999 X




Refugia PJ X

Channel Cond & Dyn

W/D Ratio

WA 1999

PJ

X

Streambank Cond. WA 1999

PJ

X


PJ

X

Flow /Hydrology

Peak/Base Flow

WA 1999 X


Watershed Cond.

Road Dens/Loc

WA 1999

PJ

X


Regime

WA 1999 X

Riparian Reserves PJ* WA 1999 X



N/A: Not Applicable

* Considered Properly Functioning on federal land and At Risk on private land

of 63

APPENDIX E Project Activities within Riparian Reserves

Table E1 provides a summary of the project activities that will occur in RRs in the project area.

The standard protection measures (BMPs, Project Design Features, Wet Weather Operations)

provide adequate protection of watershed and aquatic resources.

Description of Project Activities in Riparian Reserves

Watershed RR adjacent to

Project Activities

occurring within

RR’s

Distance from

Anadromous

Fish Habitat

PDF specific to

unit.

Otherwise see

table 2.1 in

Johnny O’Neil

Project DEIS

for list of PDFs

applicable for

all units

Effects to stream

shade/temperature

and/or suspended

sediment, stream

substrate and

embeddedness

within

anadromous fish

habitat

O’Neil Creek 7th field O’Neil Creek Habitat

restoration,

removal of the

boulder cascade

barrier, riparian

planting/reseeding,

water drafting

0.00 miles No effect to

effective stream

shade.

Insignificant

negative short term

effects and long

term positive

effects for

suspended

sediment, stream

substrate and

embeddedness, and

riparian reserves.

Bittenbender Creek-

Klamath River

Klamath River Habitat

restoration,

removal of the

boulder cascade

barrier, riparian

planting/reseeding,

water drafting

0.00 miles No effect to stream

shade.

Insignificant

negative short term

effects and long

term positive

effects or

suspended

sediment, stream

substrate and

embeddedness, and

riparian reserves.

of 63

Appendix F: Life History and Biological Requirements

of Pacific Salmonids The Bittenbender Creek-Klamath River 6

th field watershed provides approximately 1.3 miles

miles of anadromous fish habitat within the analysis area distributed within the main stem,

Klamath River and O’Neil Creek for the following Evolutionarily Significant Units of Pacific

salmonids: fall run Upper Klamath-Trinity Rivers Chinook salmon (Oncorhynchus tshawytscha),

winter run Klamath Mountain Province steelhead (O. mykiss) and Southern Oregon/Northern

California Coasts (SONCC) coho salmon (O. kisutch). The following Pacific salmonid

Evolutionary Significant Units and their habitat in the Klamath River basin have special status

under the Endangered Species Act (ESA) or are given special management consideration as

Forest Service Sensitive Species:

Endangered: None

Threatened: SONCC coho salmon

Critical Habitat: SONCC coho salmon

Proposed: None

Sensitive: Upper Klamath-Trinity Rivers Chinook salmon;

Klamath Mountains Province steelhead

Essential Fish Habitat: SONCC coho salmon; Upper Klamath-Trinity

Chinook salmon

Coho Salmon

General life history information and biological requirements of Southern Oregon/Northern

California Coastal (SONCC) coho salmon have been described in various documents

(Shapovalov 1954; Hassler 1987; Sandercock 1991; Weitkamp et al. 1995) as well as NOAA-

Fisheries’ final rule listing SONCC coho salmon (May 6, 1997; 62 FR 24588). Adult coho

salmon typically enter rivers between September and February. However, the Academy of

Sciences, 2002 report offer more specific information for the Klamath River mainstem:

Coho salmon enter the main stem of the Klamath River for spawning typically in their third year,

primarily between October and December. Over most of this interval, main-stem flows below

Iron Gate Dam often are high (ca. 2500-3000 cfs). Thus, standard methods for observing and

counting spawning fish are not easily applied, and the size of the spawning population is

unknown. Approximations put the entire ESU at about 10,000 spawning coho salmon of non-

hatchery origin per year (Weitkamp et al. 1995), of which only a small portion is associated with

the Klamath Basin, where several important tributary runs have been reduced to a handful of

individuals. Although a minor amount of spawning and growth may occur in the main stem, the

main stem serves adults primarily as a migration route

(http://www.klamathbasincrisis.org/articles/NAS-Report/nas_chapter3-coho.htm).

Spawning occurs from November to January (Hassler 1987) in the tributaries to the Klamath

River, but occasionally as late as February or March (Weitkamp et al. 1995). Coho salmon eggs

incubate for 35-50 days between November and March. Successful incubation depends on

several factors including dissolved oxygen levels, temperature, substrate size, amount of fine

sediment, and water velocity. Fry start emerging from the gravel two to three weeks after

of 63

hatching and move into shallow areas with vegetative or other cover. As fry grow larger, they

disperse up or downstream. In summer, coho salmon fry prefer pools or other slower velocity

areas such as alcoves, with woody debris or overhanging vegetation. Juvenile coho salmon over-

winter in slow water habitat with cover as well. The proposed Project will improve and increase

both over-summering and over-wintering habitat by creating a pond at the junction of O’Neil

Creek and the Klamath River. Juveniles may rear in fresh water for up to 15 months then

migrate to the ocean as smolts from March to June (Weitkamp et al. 1995). Coho salmon adults

typically spend two years in the ocean before returning to their natal streams to spawn as three-

year olds.

Available historical and most recent published coho salmon abundance information are

summarized in the NOAA-Fisheries coast-wide status review (Weitkamp et al. 1995). The rivers

and tributaries in the California portion of this ESU were estimated to have average recent runs

of 7,080 natural spawners and 17,156 hatchery returns, with 4,480 identified as native fish

occurring in tributaries having little history of supplementation with non-native fish. However,

limited information exists regarding coho salmon abundance in the Klamath River basin. What

information exists [CDFG unpublished data; U.S. Fish and Wildlife Service (USFWS)

unpublished data] suggests adult populations are small to nonexistent in most years. The decline

of SONCC coho salmon across the ESU is not the result of one single factor, but rather a number

of natural and anthropogenic factors that include dam construction, instream flow alterations;

land use activities coupled with large flood events, fish harvest and hatchery effects.

Little is known about Coho populations in O’Neil Creek. NOAA Fisheries (2008) concluded

that though information was lacking, available information indicates coho populations are

depressed. Using an adult-to-smolt relationship, CDFG (2007) projected very low abundances of

adult coho salmon returning to the Shasta River Basin in 2007 (54 adults) and 2008 (37 adults).

The assumption, therefore is that the trends in Coho populations are basin or system wide, and

numbers in O’Neil Creek and within the project area have also declined and remain depressed.

The KNF refined the GIS steelhead trout distribution layer to determine SONCC coho salmon

CH and SONCC coho salmon and UKT Chinook salmon EFH, using field observation to

determine occupied habitat. Based on the range of steelhead mapped by the KNF, CH/EFH

occurs in the Action Area. In the anadromous fish bearing streams that may be affected by PEs,

CH occurs in the lower 0.5 miles of O’Neil Creek, and in the portion of the Klamath River

within the Action Area. This portion of the Klamath River within the Action Area begins at the

confluence with O’Neil Creek and extends approximately 0.8 miles downstream to the

confluence with Louie Creek.

Chinook Salmon

The following information was excerpted or summarized from NMFS status review of Chinook

salmon (Meyers et al. 1998). Chinook salmon mature between 2 and 6+ years of age (Meyers et

al. 1998). Fall-run Chinook salmon enter freshwater at an advanced stage of maturity, move

rapidly to their spawning areas on the mainstem or lower tributaries of the rivers, and spawn

within a few days or weeks of freshwater entry (Healey 1991). Post-emergent fry seek out

shallow, nearshore areas with slow current and good cover, and begin feeding on small terrestrial

and aquatic insects and aquatic crustaceans. The optimum temperature range for rearing

of 63

Chinook salmon fry is 50°F to 55°F (Rich 1997, Seymour 1956) and for fingerlings is 55°F to

60°F (Rich 1997). In preparation for their entry into a saline environment, juvenile salmon

undergo physiological transformations known as smoltification that adapt them for their

transition to salt water. The optimal thermal range for Chinook salmon during smoltification and

seaward migration is 50°F to 55°F (Rich 1997). Chinook salmon spend between one and four

years in the ocean before returning to their natal streams to spawn (Meyers et al. 1998). Chinook

salmon addressed in this document exhibit an ocean-type life history, and smolts out-migrate

predominantly as subyearlings, generally during April through July. Chinook salmon spend

between 2 and 5 years in the ocean (Healey 1991), before returning to freshwater to spawn.

Some Chinook salmon return from the ocean to spawn one or more years before full-sized adults

return.

The UKT ESU includes fall- and spring-run Chinook salmon in the Klamath and Trinity River

Basin upstream of the confluence of the Klamath and Trinity rivers. Historically, spring-run

Chinook salmon were probably the predominate run. This ESU still retains several distinct

spring-run populations, albeit at much reduced abundance levels. Fish from this ESU exhibit an

ocean-type life history; however genetically and physically, these fish are quite distinct from

coastal and Central Valley Chinook salmon ESUs. Genetic analysis indicated that this ESU form

a unique group that is quite distinctive compared to neighboring ESUs. The majority of spring-

and fall-run fish emigrate to the marine environment primarily as subyearlings, but have a

significant proportion of yearling smolts. Recoveries of coded wire tags indicate that both runs

have a coastal distribution off the California and Oregon coasts.

The project is located in the O’Neil Creek watershed. O’Neil Creek provides regionally

significant habitat for anadromous fishes, including SONCC coho salmon, and KMP steelhead

trout. The portion of the Klamath River in the Bittenbender Creek-Klamath River 6th

field

watershed provides regionally significant habitat for anadromous fishes, including SONCC coho

salmon, UKT fall-run Chinook salmon, and KMP steelhead trout.

Steelhead

Biologically, steelhead can be divided into two basic run-types, based on the state of sexual

maturity at the time of river entry and duration of spawning migration (Burgner et al. 1992). The

stream-maturing type, or summer steelhead, enters fresh water in a sexually immature condition

and requires several months in freshwater to mature and spawn. The ocean-maturing type, or

winter steelhead, enters fresh water with well-developed gonads and spawns shortly after river

entry (August 9, 1996, 61 FR 41542; Barnhart 1986). South of Cape Blanco, Oregon, summer

steelhead are known to occur in the Rogue, Smith, Klamath, Trinity, Mad, and Eel rivers, and in

Redwood Creek (Busby et al. 1996).

Winter steelhead enter fresh water between November and April in the Pacific Northwest (Busby

et al. 1996; Nickelson et al. 1992), migrate to spawning areas, and then spawn, generally in April

and May (Barnhart 1986). Some adults, however, do not enter some coastal streams until spring,

just before spawning (Meehan 1991). Steelhead require a minimum depth of 0.18 m and a

maximum velocity of 2.44 m/s for active upstream migration (Smith 1973). Spawning and initial

rearing of juvenile steelhead generally take place in small, moderate-gradient (generally 3-5%)

tributary streams (Nickelson et al. 1992). A minimum depth of 0.18 m, water velocity of 0.30-

of 63

0.91 m/s, and clean substrate 0.6-10.2 cm (Nickelson et al. 1992) are required for spawning.

Steelhead spawn in 3.9-9.4°C water (Bell 1986). Depending on water temperature, steelhead

eggs may incubate for 1.5 to 4 months (August 9, 1996, 61 FR 41542) before hatching, generally

between February and June (Bell 1986). After two to three weeks, in late spring, and following

yolk sac absorption, alevins emerge from the gravel and begin actively feeding. After emerging

from the gravel, fry usually inhabit shallow water along banks of perennial streams. Fry occupy

stream margins (Nickelson et al. 1992). Summer rearing takes place primarily in the faster parts

of pools, although young-of-the-year are abundant in glides and riffles. Winter rearing occurs

more uniformly at lower densities across a wide range of fast and slow habitat types. Productive

steelhead habitat is characterized by complexity, primarily in the form of large and small wood.

Some older juveniles move downstream to rear in larger tributaries and mainstem rivers

(Nickelson et al. 1992). Steelhead prefer water temperatures ranging from 12-15°C (Reeves et

al. 1987). Juveniles live in freshwater from one to four years (usually two years in the California

ESUs), then smolt and migrate to the ocean in March and April (Barnhart 1986). Winter

steelhead populations generally smolt after two years in fresh water (Busby et al. 1996).

The KMP steelhead ESU occurs in coastal river basins between the Elk River in Oregon and the

Klamath River in California, inclusive. The KMP steelhead ESU contains populations of both

winter and summer steelhead. The Rogue and Klamath River basins are distinctive in that they

are two of the few basins producing “half-pounder” steelhead. In 2001, NOAA-Fisheries

reconsidered the status of KMP steelhead under the ESA (66 FR 17845, April 4, 2001) and

determined that KMP steelhead do not warrant listing as threatened or endangered at this time.

In California, the largest proportions of naturally spawning hatchery fish are believed to occur in

the Trinity River, where estimates from 1990s range from 20-70 percent hatchery. These

estimates apply to fall-run fish. Because the hatchery program in the Trinity River basin

propagates mostly fall-run fish, natural spawners in this basin that return at other times are

believed to be predominantly of natural origin. Counts at Willow Creek weir provide an estimate

of about 2000 natural origin fall-run spawners per year. The Willow Creek weir samples

steelhead only over a period of about 3 months during the fall run and thus provides no

information about other runs in the basin. CDFG biologists estimated natural escapement in the

California portion of the ESU to be approximately 30,000-50,000 adults per year.

Designated Critical Habitat for coho salmon

Designated CH for coho salmon encompasses accessible reaches of all rivers (including estuarine

areas and tributaries) between the Mattole River in California and the Elk River in Oregon,

inclusive (May 5, 1999, 64 FR 24049). The area described in the final rule represented the

current freshwater and estuarine range of coho salmon. Land ownership patterns within the coho

salmon ESU analyzed in this document and spanning southern Oregon and northern California

are 53% private lands; 36% Federal lands; 10% State and local lands; and 1% Tribal lands. The

Forest Service manages about 1,680,000 acres (90.6%) of land within the Forest boundaries and

about 200,000 acres (9.4%) of land are within the Forest boundaries but in other ownership

(LRMP, Page 3-12. USDA Forest Service 1995)).

The KNF recognizes that coho and Chinook salmon may not occupy the same waters as

of 63

steelhead because of the difference in jumping abilities. The maximum jumping height for coho

is 2.2 meters; Chinook salmon is 2.4 meters; and steelhead is 3.4 meters (Meehan, 1991).

Therefore, steelhead can access more habitat than coho or Chinook salmon. The use of the KNF

steelhead distribution layer to define coho salmon CH is, therefore, recognized as a conservative

approach for assessment of effects to coho salmon CH.

biological assessment for threatened, endangered, proposed,...

Documents