quality assurance project plan...

QUALITY ASSURANCE

PROJECT PLAN (QAPP)

For

Monitoring ecosystem response to restoration and climate change in the Snohomish River estuary.

Jan 2013

QAPP for Monitoring ecosystem response to restoration and climate change in the Snohomish River estuary.

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2. TABLE OF CONTENTS

1. APPROVAL OF QAPP: ...................................................................................................................... 2

2. TABLE OF CONTENTS .................................................................................................................... 3

3. PROJECT MANAGEMENT .............................................................................................................. 4

DISTRIBUTION LIST ........................................................................................................................... 4

PROJECT TASK/ORGANIZATION ..................................................................................................... 4

PROBLEM DEFINITION/BACKGROUND ......................................................................................... 4

PROJECT TASK DESCRIPTION.......................................................................................................... 5

DATA QUALITY OBJECTIVES AND MEASUREMENTS CRITERIA ............................................ 9

SPECIAL TRAINING AND CERTIFICATION ................................................................................. 10

DOCUMENTS AND RECORDS ......................................................................................................... 11

4. DATA GENERATION AND ACQUISITION ................................................................................. 12

SAMPLING PROCESS DESIGN (Experimental Design) ................................................................... 12

SAMPLING METHODOLOGY .......................................................................................................... 13

SAMPLE HANDLING AND CUSTODY ........................................................................................... 15

ANALYTICAL METHODS ................................................................................................................. 16

QUALITY CONTROL ......................................................................................................................... 16

INSTRUMENT/EQUIPMENT TESTING, INSPECTION AND MAINTENANCE .......................... 16

INSTRUMENT/EQUIPMENT CALIBRATION AND FREQUENCY .............................................. 16

INSPECTION/ACCEPTANCE OF CONSUMABLE SUPPLIES ...................................................... 16

NON-DIRECT MEASUREMENTS (SECONDARY DATA)............................................................. 17

DATA MANAGEMENT ...................................................................................................................... 17

5. ASSESSMENTS AND RESPONSE ACTIONS .............................................................................. 17

REPORTS TO MANAGEMENT .......................................................... Error! Bookmark not defined.

6. DATA VALIDATION AND USABILITY ...................................................................................... 18

VERIFICATION AND VALIDATION METHODS ........................................................................... 18

RECONCILIATION WITH USER REQUIREMENTS....................................................................... 18

7. REFERENCES .................................................................................................................................. 19


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3. PROJECT MANAGEMENT

DISTRIBUTION LIST

Copies of the completed/signed project plan and reports shall be distributed to:

Name Title Affiliation E-Mail Phone QAPP Report

Todd Zackey Principal

Investigator

Tulalip

Tribes

[email protected] 360-716-

4637

x x

Joshua Kubo Project

Manager

Tulalip

Tribes

[email protected] 360-716-

4638

x x

Dr. Casey Rice Co-PI NOAA [email protected] 425-347-

6935 x231

x x

Joshua Chamberlin Co-PI NOAA [email protected] 206-302-

2472

x x

Jason Hall Co-PI NOAA [email protected] 206-302-

1748

x x

Jason Schilling Co-PI Tulalip

Tribes

jschilling@tulaliptribes-

nsn.gov

360-716-

4611

x x

Tiffany Waters QA NWIFC [email protected] 360-528-

4318

x

Lisa Chang R10 QAM EPA [email protected] 206-553-

0226

x

PROJECT TASK/ORGANIZATION The following individuals comprised the project team with responsibilities for the design and

implementation of this project:

Todd Zackey, Principal Investigator, is the main point of contact and shall have the over-all

responsibility for the implementation of the project. He shall ensure that the project shall adhere to all

the objectives, protocols and timeline specifications of the EPA approved QAPP.

Joshua Kubo, Project Manager, will be responsible for project reporting, grant budget management, and

assuring all grant requirements are met.

Dr. Casimir Rice, Joshua Chamberlin, Jason Hall, Jason Schilling, Co-investigators, are responsible for

key components of the project. Dr. Rice and Joshua Chamberlin are responsible for fish sampling and

field coordination, Jason Hall is responsible for hydrology, and Jason Schilling is responsible for birds.

Ginna Grepo-Grove, Lisa Chang: The USEPA Quality Assurance Manager is Ginna Grepo-Grove. She

or her designee will review and approve the QAPP and subsequent addendums or amendments to the

QAPP submitted to the USEPA. NWIFC’s EPA Project Officer is Lisa Chang and she is responsible for

mailto:[email protected]







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interfacing with NWIFC to oversee that the overall grant conditions are met in accordance with the

NWIFC EPA contract.

Tiffany Waters, Lucy Yanez: The NWIFC Puget Sound Recovery Project Coordinator is Tiffany Waters

and the Contracts Specialist is Lucy Yanez. NWIFC shall administer the EPA-sponsored grant sub-

award and shall be responsible for the oversight of the contract, ensuring that the goals and objectives of

the project are achieved. They will ensure that project deliverables are complete and of necessary quality

and that the project completion dates are met. They will interface with the USEPA regarding the status

of the approved project.

PROBLEM DEFINITION/BACKGROUND Protection and recovery of the Snohomish River estuary is a high priority for Tulalip Tribes

because the existence and persistence of salmon and other natural resources dependent on the estuary are

integral for the tribe to maintain its cultural identity and subsistence. For example, with several salmon

stocks (including wild Chinook, the most estuary dependent of all salmon) diminished throughout

Tulalip’s usual and accustomed fishing areas, significant investments in salmon recovery are necessary

to support tribal fisheries and Treaty Rights. High priority activities such as estuarine protection and

restoration are therefore a reserved treaty right and strongly supported by Tulalip and other Puget Sound

Tribes. In order to ensure the future of estuary-dependent components of the Tribes’ natural heritage,

scientific information is necessary to understand how the Snohomish estuary ecosystem works, how it

responds to anthropogenic stressors such as climate change, and whether actions intended to improve

ecological condition are effective. Extensive, estuary-wide monitoring efforts are a clear priority of the

Tulalip Tribes, and the proposed work addresses this need.

The Snohomish River estuary is the second largest in the Puget Sound and provides habitat for Chinook

and other salmonids (Snohomish Basin Salmon Recovery Forum 2005). These estuarine rearing and

migration areas are necessary in the transition from freshwater to the critically important first year at

sea. Similarly, estuaries provide vital habitat for a myriad of resident, migratory, and overwintering bird

populations (City of Everett 2001, Wentworth-Davis 2011). The massive loss and degradation of

juvenile salmonid habitat in the Snohomish estuary, as a result of modern human activities, was

identified in the Snohomish Basin Recovery Plan as the primary factor limiting Chinook salmon survival

in the basin (Snohomish River Basin Salmon Conservation Plan 2005). Additionally, degraded estuarine

habitat conditions combined with a changing climate and sea level rise have been identified as threats to

Puget Sound avian assemblages (Audubon 2009). Fortunately, the Snohomish estuary has high potential

for wild Chinook and avian recovery through restoration of estuarine wetlands, where over 1200 acres

have been restored or identified as potential restoration projects. Coupled with extensive restoration

actions is the need for ongoing monitoring throughout the estuary to track individual and cumulative

effectiveness of restoration projects, and to determine the condition of Snohomish estuarine habitats in

response to continuing anthropogenic stressors, including climate change. All ecosystem and salmon


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recovery planning efforts recognize the need for monitoring (e.g., Snohomish River Basin Salmon

Conservation Plan 2005, Puget Sound Partnership Action Agenda 2012, Snohomish Basin 3-year Work

Plan 2012) but such efforts are rare. In addition, bird surveys will achieve monitoring goals outlined in

the Washington Wildlife Conservation Strategy (WDFW and the North American Marsh Bird

Monitoring Program (Conway 2011). Many stakeholders and individual projects would benefit from

comprehensive monitoring efforts, yet little coordination and collaboration occurs. The comprehensive

monitoring plan for the Qwuloolt project (Rice et al. 2011) provides a template for project level

restoration monitoring in the Snohomish that addresses a wide array of abiotic (e.g., land forms,

hydrology) and biotic (vegetation, invertebrates, birds, fishes, and mammals) attributes, and is now

informed and refined by three full years of implementation. We propose to facilitate effective project

level monitoring continue and expand system-wide monitoring efforts in support of the restoration and

recovery of the Snohomish River estuary by: 1) ensuring the continuation of basic, ongoing fish

monitoring; 2) continuing avian monitoring at reference and project sites; 3) installation of additional

hydrologic and elevation/sedimentation monitoring equipment; and 4) expanded system-wide and

project level monitoring through outreach and planning activities to increase participation by more

stakeholders, and acquire additional funding. As noted above, the proposed efforts are relevant to at least

eight Puget Sound Action Agenda items.

PROJECT TASK DESCRIPTION This research project will examine several components of the ecosystem across the estuarine landscape

to help evaluate restoration effectiveness and response to climate change. We will quantify seasonal

abundance and composition of both fish and bird communities, as well as assess the individual condition

juvenile salmon. The proposed project is particularly relevant to a number of objectives under the Puget

Sound Action Agenda Strategic Initiative: Protection and Restoration of Habitat.

General Project Timeline

The project is broken in to four specific tasks which will largely be conducted simultaneously

throughout the funding period with the exception of the development of the Quality Assurance Project

Plan which will be finalized and approved prior to data collection.

TASK/MILESTONE OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP

1. Project Management

2. QAPP Development

3. Planning and Outreach

4. Data Collection

5. Analysis and Writing


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Project Tasks

Planning and Outreach. The proposed project is intended to inform WRIA 7 stakeholders and

Snohomish Estuary project proponents of the existing and future ecological conditions of the Snohomish

River system. A goal of this project is to ensure that the proper information is collected to allow

stakeholders and project proponents to implement adaptive management strategies to ensure the

successful recovery of the Snohomish River watershed. This project seeks to develop a cooperative and

coordinated effort, pooling resources from all Snohomish estuary stakeholders and project proponents.

The aim of the coordination is to conduct effective and relevant monitoring efforts, fill data gaps,

implement adaptive management in light of changing climatic conditions, and seek further support to

continue the necessary monitoring needs of the Snohomish estuary. Information and collaboration

among stakeholders and project proponents will be organized by the Snohomish Basin Capital Programs

Coordinator (Morgan Ruff, Tulalip tribes) and disseminated through the Snohomish Estuary Working

Group. These efforts will help to promote a consistent, effective, efficient, and long-term monitoring

from project level to system-wide efforts. The Estuary Working Group will provide an ideal forum for

sharing this information, aligning current monitoring efforts, and collaborating for future strategies. A

workshop on monitoring results and strategies will be conducted early in the project and a report will be

produced at the end.

Data Collection. Data collection will begin upon EPA approval of the QAPP and will be conducted by

Tulalip Staff, PI, Wildlife Biologist, Field Technician, Field Biologist, NOAA NWFSC staff, and

volunteers. NOAA NWFSC will be sub-contracted to assist with the data collection effort and additional

funding resources will be used to fund Tulalip staff for data collection efforts. Data will be collected to

assess the current conditions across the Snohomish Estuary system, long-term monitoring sites will be

establish for assessing and tracking long-term changes in the estuary, and efforts will be made to assist

in the development of predictive models (e.g. Battelle’s Finite Volume Coastal Ocean Model, USGS

rapid assessment protocol (RAP) for Potential Sediment Accretion) which assess future climate change

implications in the Snohomish watershed. Across the estuary, biological data will be collected for birds

and fish, hydrological conditions will be assessed utilizing water column profiling instruments, and

longterm sediment conditions will be monitored utilizing sediment surface elevation tables (SET) sites

located across the estuary. Data collection sub-tasks are as follows:

Data Collection Sub-Tasks

OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP

Fish Sampling

Bird Surveys

Hydrologic Data Loggers

Water Profiling

SET Installation/ Sampling


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1) Fish. NOAA’s Northwest Fisheries Science Center (NWFSC) has been monitoring fish in the

Snohomish estuary for over a decade in collaboration with Tulalip Tribes. This work has never received

substantial dedicated funding and was suspended in 2011. Through a restoration monitoring

collaboration between NOAA and the Tulalip Tribes, year-round estuary-wide monitoring was resumed

in 2012 with significant improvements in the sampling scheme, including full coverage of the estuary

from tidal freshwater to nearshore, and stratified random site selection. Application and development of

a system-wide monitoring template has been closely related to intensive, pre-breach monitoring

strategies conducted at the Qwuloolt restoration site (Rice et al. 2011) by NOAA/NWFSC and Tulalip

Tribes since 2009. Additionally, the overall monitoring approach is consistent with recommendations

being developed to evaluate regional salmon recovery efforts (Puget Sound RITT, 2012) and is based on

the extensive work done in the Skagit River estuary (e.g., Beamer et al. 2005) that the NWFSC has been

a contributor to since 2001. Through the implementation of a system-wide monitoring strategy in the

Snohomish, this project aims to expand long-term monitoring efforts and further develop a rigorous

monitoring program of habitat (e.g., hydrology and sediment) and biota (e.g. fish and bird). A key

component of this proposal is to expand and formalize collaborations with other lead entities in the area

(e.g. Snohomish County), coordinating project level monitoring, and integrating it into estuary-wide

efforts.

2) Birds. Bird surveys were initiated in 2012 for the purpose of assessing marsh bird and overall avian

abundances before and after tidal inundation in the Qwuloolt restoration project area. Marsh bird

abundance and distribution over space and time indicate habitat quality and can be used as measures of

restoration success (Neckles et al. 2002, U. S. EPA 2002). Combined with a similar USGS study in the

Nisqually estuary, this bird monitoring effort will contribute to a region-wide effort comparing effects of

restoration on birds in the Puget Sound. In addition to measuring the effects of restoration on avian

assemblages, this study will also contribute to a national and regional database of marsh bird population

assessments. Tidal salt marsh bird populations are currently undersampled and in need of a focused

monitoring effort (Conway and Droege 2006). Standardized monitoring protocol for marsh birds has

been developed (Conway and Droege 2006, Conway et al. 2011) to facilitate a large-scale monitoring

effort and database for assessing regional or range-wide population trends and identifying declining

species before they become endangered. Efforts for this project aim to provide a baseline dataset from

restoration projects (e.g. Qwuloolt & Smith Island) and reference sites for monitoring effects of climate

change and predicted sea-level rise on avian assemblages and marsh dependent birds in the Snohomish

estuary.

3) Hydrology. Limited monitoring of basic hydrology has been conducted by NOAA/NWFSC and

Tulalip Tribes; including discrete water column profiling and continuous water level, salinity, and

temperature monitoring within the Snohomish estuary. While these efforts have been limited in spatial

and temporal extent, the data collected thus far have provided useful insights into the dynamic salinity

gradients within the estuary and the relationships between tides, river flow, salinity, and temperature,

and established pre-restoration “baseline” conditions across the estuary. Hydrology is a key driver of

estuarine ecosystems and expanding both the spatial and temporal coverage of hydrological monitoring

within the Snohomish estuary would provide several major benefits: (1) improve our understanding of

existing physical and biological patterns within the estuary, (2) provide baseline and response data to

evaluate restoration effectiveness and responses within the estuary, and (3) provide calibration data to

refine previously developed hydrodynamic models (e.g. Battelle’s Finite Volume Coastal Ocean Model,


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USGS rapid assessment protocol (RAP) for Potential Sediment Accretion)to evaluate potential climate

change impacts within the estuary.

With these benefits in mind, we propose water column sampling using CTD profilers during key

flow and tide stages (e.g., spring and neap tide series; high and low tide stages; and high, average, and

low flow conditions) at previously sampled stations in the mainstem and Ebey Slough, as well as

expansion into previously omitted sections of Steamboat, Union, and Ebey Sloughs. Additionally, we

propose installation of continuous water level, salinity, and temperature sensors at previously monitored

stations in Ebey Slough as well as additional sensors at key hydrological bifurcations and gradients (as

delineated from previous water column profile data) within the system. In addition to improving our

understanding of existing physical and biological patterns, and providing baseline and response data for

restoration actions, these hydrological data can be used to refine and expand the temporal and spatial

calibrations for the Finite Volume Coastal Ocean Model (FVCOM) that was developed for the

Snohomish estuary in 2006 (Yang and Khangaonkar 2008). In combination with a larger scale

circulation model of Puget Sound that is capable of nesting the Snohomish River estuary FVCOM

model (Khangaonkar et al. 2011), temporal and spatial expansions of hydrological calibration data can

be used to evaluate longer term estuary responses to forcing from Puget Sound and potential climate

change scenarios. Future hydrologic loading scenarios using IPCC A1b and B2 emissions scenarios

downscaled to the Pacific Northwest can be used in combination with the nested Snohomish River

estuary FVCOM model to assess the sensitivity of hydrodynamic and water quality parameters to

climate change stressors. For example, these scenarios could be used to evaluate the impacts of potential

reductions in summer flows coupled with sea level rise due to climate change, which could result in

upstream propagation of salinity and loss of brackish tidal marsh habitat.

4) Sediment Dynamics. A key determinant of coastal wetland vulnerability to sea level rise (SLR) is

whether the surface elevation in the intertidal zone can keep pace with sea level rise. It is crucial to

quantify the vertical movement of coastal wetland surfaces, which will help identify sites under threat

from SLR, thus informing conservation, mitigation and adaptation. The USGS is establishing a network

of coastal marsh monitoring sites in the Pacific Northwest and California during 2012 and 2013 to assess

the vulnerability of these coastal wetlands to changes in sea -level rise (Guntenspergen personal

communication). Rod Surface Elevation Table - Marker Horizon method (RSET and SET-MH) is the

method used. Because of funding limitations only one site has so far been established in Puget Sound -

Nisqually National Wildlife Refuge in the southern portion of the Sound. In addition to the USGS effort,

researchers at Western Washington University have SET sites in northern Puget Sound (Kairis and

Rybczyk 2010). Establishment of the SET/MH sites at Qwuloot and across the Snohomish River Estuary

would provide valuable additional information not only for the Snohomish, but for these larger efforts

and increase the generality of the results. Previous studies have revealed high across-site variability in

the processes that contribute to surface elevation change, making assumptions of uniformity in processes

across wetlands inappropriate. This highlights the need for site-specific data across a network of sites

that accurately represent local processes in order to evaluate the outcome of different sea level rise

scenarios.

DATA QUALITY OBJECTIVES AND MEASUREMENTS CRITERIA Data Quality Objectives (DQOs) are the quantitative and qualitative terms field personnel and project

managers use to describe how good the data needs to be in order to meet the project’s objectives. DQOs

for measurement data (referred to here as data quality indicators) are precision, accuracy,


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representativeness, completeness, comparability, and measurement range. The overall QA objective for

analytical data is to ensure that data of known and acceptable quality are provided. To achieve this goal,

data must be reviewed for 1) representativeness, 2) comparability, 3) precision, 4) accuracy (or bias),

and 5) completeness. Precision, accuracy, completeness, sample representativeness and data

comparability are necessary attributes to ensure that analytical data are reliable, scientifically sound, and

legally defensible.

Representativeness is the degree to which data from the project accurately represent a particular

characteristic of the environmental matrix which is being tested. Our study design helps insure

representativeness by stratifying both random and index sites across the estuarine landscape as a

function of channel length and connectivity. Index sites are distributed across the major estuarine

zones/habitat types (Cowardin et al. 1979) and are supplemented by randomly selecting additional sites

within each zone. Our year-round sampling design ensures we have sufficient temporal coverage. Sites

selected to monitor hydrology throughout the system were selected to represent the major transition

areas (e.g. channel bifurcations) as informed by previous data collection and model development

(Khangaonkar et al. 2011). Bird count and sediment dynamics survey designs will incorporate sites

within, and adjacent to, the project and reference sites and represent different habitat types along an

elevation gradient.

Comparability is the measurement of the confidence in comparing the results of one sampling event

with the results of another achieved by using the same matrix, sample location, sampling techniques and

analytical methodologies. Our survey design employs index sites to be repeatedly sampled, and our

twice monthly sampling program ensures we sample on a similar tides series to reduce sources of

temporal variation.

Accuracy and Precision: Accuracy is the degree to which samples reflect the true value of the system,

and bias can be measured as a difference from the true estimate. Precision is the degree to which

separate measurements agree. While it is difficult to evaluate accuracy and precision for some measures

because of tradeoffs with representative and completeness, we will use methods that have been cross-

validated with similar projects throughout Puget Sound and will operate and maintain technical

equipment according to manufacturer’s standards as outlined in the Quality Control section below.

Completeness: Our stratified random survey design which incorporates index sites strives for

completeness by sampling throughout the year across several environmental gradients representative of

the system.

SPECIAL TRAINING AND CERTIFICATION

The project team has extensive experience working in the project area using collection methods as

outlined in the proposed study. All primary field personnel have current cpr and first aid certifications,

small boat handling training, and have completed all health and safety requirements as identified by their

respective employers.

Todd Zackey is the Marine and Nearshore Program Manager for the Tulalip Tribes Natural Resources

Department and has been working for the Tribes for over a decade. He manages the GIS (Geographic

Information Systems) and Nearshore Programs for the department and is responsible for mapping,


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monitoring, assessing, and protecting the Tribes’ nearshore and marine resources on and off the

reservation. Todd has conducted and been involved in a variety of monitoring and research projects in

the nearshore areas of the Whidbey Basin including water quality monitoring, mapping of intertidal

habitat, and studying juvenile salmon utilization of the Snohomish River estuary, pocket estuaries, and

small coastal streams. Todd is a member of the San Juan Salmon Technical Advisory Group, and Co-

Chair of the Island County Salmon Technical Advisory Group.

Joshua Kubo is the Salmon Recovery Scientist for the Tulalip Tribes Natural and Cultural Resources

Department.

Dr. Casimir Rice has been studying anthropogenic impacts in Puget Sound at NWFSC since 1990 and

has extensive experience monitoring and evaluating nearshore marine and estuarine ecosystems. He

currently is managing monitoring efforts in the Snohomish estuary and has led the effort to develop an

adaptive monitoring plan for the Qwuloolt restoration project.

Joshua Chamberlin is a fisheries biologist at NWFSC with 9 years of experience studying the ecology

of nearshore marine and estuarine ecosystems in Puget Sound. He has been involved in monitoring

efforts in the Snohomish River estuary since 2005 and currently coordinates field collection activities for

the Qwuloolt restoration project and Snohomish system-wide monitoring effort.

Jason Hall is fisheries biologist at NWFSC with 11 years experience in fisheries research in the Puget

Sound. He began working in the Snohomish River estuary in 2009 and has been involved in fish and

hydrology monitoring, RTK GPS surveys, and GIS analyses associated with the Snohomish system-

wide monitoring effort.

Jason Schilling is a wildlife biologist with the Tulalip Tribes.

DOCUMENTS AND RECORDS Complete documentation for field sampling teams may include but is not limited to the following forms:

Site sampling data records

Sample container labels

Field sampling log books

Data collected for fish sampling and hydrology will be electronically entered into a Filemaker Pro

database. All samples will be referenced using a numbering system allowing cross-reference to site and

date sampled. Data will be stored electronically at the NWFSC and with the Tulalip Tribe. In the event

of computer malfunction, paper datasheets will be available for data entry. Field Teams will maintain

field notes and all documents and data collected will be assessed after each sampling to maintain proper

QA/QC measures. Individual samples taken for further processing at the NWFSC lab will be given

unique sample numbers and individual labels that identify both individual and site/sampling parameters

will be attached to all samples.


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Bird count and sediment dynamics data will be recorded in field logs and entered into a digital format

upon completion of each sampling event. Digital copies will be distributed among the PI, project

manager, and contracted staff.

The PI will be responsible for sharing copies of the final QAPP with all members of the research team.

4. DATA GENERATION AND ACQUISITION

SAMPLING PROCESS DESIGN (Experimental Design)

Study Site Selection

Sites selection and sample design were created using several different criteria and existing datasets

depending on the type of sample collection or task. Below are the procedures as they pertain to each

component of data collection:

1) Fish: A combination of index and random monitoring stations were used to monitor fish within

the Snohomish River estuary. Index site locations were based on previously sampled index sites

which were known to be fishable with a beach seine. Random monitoring stations were

randomly selected from a GIS derived polyline of fishable shorelines. This polyline layer was

derived from aerial RGB orthophotos taken during a 2009 LiDAR survey of the Snohomish

River estuary during a low tide. The polyline layer was further classified by functional habitat

zones and allocation of random sites drawn per sampling event was based on the relative

proportions of calculated shoreline within each habitat zone. A minimum distance of separation

between points of 150 m was enforced for all random draws within each sampling event.

2) Bird Counts: See sampling methodology below...

3) Hydrology: Vertical water profile sample stations were established from the estuary mouth at

Jetty Island to the town of Snohomish within the main river and distributary network; including

the mainstem river, Ebey Slough, Steamboat Slough, and Union Slough (where accessible by

boat at high and low tide). The sample stations were distributed throughout the sample area with

approximately 1 km spacing between stations. Continuous water level logger stations were

established at the main bifurcations of the system and at key transitional hydrology zones as

identified by previous monitoring and modeling efforts.

4) Sediment Dynamics: Sites selected for monitoring sediment dynamics will be chosen to

represent various habitat types along an elevation gradient both within, and adjacent to, the

project site. Consultation with USGS scientists will occur in early 2013 to finalize the sampling

plan which will be submitted for review and approval.


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SAMPLING METHODOLOGY

Fish

Beach seines will be used to sample "mainstem" habitats throughout the Snohomish River estuary.

Sampling will occur twice per month between February and September and then once a month between

October and January. We will use standard Puget Sound beach seine measuring 36m in length and 1.8m

(wings) to 3.0m (bag) in height made of 3mm (wings) to 1.5mm (bag) knot-less nylon mesh. The seine

is set in a semi-circle from upstream to downstream with one end held on shore and the other set from

the boat. Once the net is set, both sides are pulled in together with 3 or 4 individuals until the entire

catch is consolidated in the bag (i.e. center of the net). Fish are immediately removed from the bag and

placed into 5-gallon buckets with fresh water from the site where they are held for processing. Up to 25

individuals of each species will be measured to fork length where applicable and to total length when no

fork is present. Any additional individuals of each species will be counted. Up to 10 each, marked and

unmarked, juvenile Chinook salmon will be taken from each zone, as described, above for further

processing. Any individuals that appear unduly stressed or dead upon retrieval of the net will be selected

before healthy individuals are sacrificed. In addition, surface water temperature and salinity will be

measured and recorded at each site using a YSI Professional Plus Mulitparameter meter.

Bird Counts

Breeding-season point count surveys will be conducted to account for focal marsh bird species (Table 1)

and all other birds. Surveys for these species will be conducted following Standardized North American

Marsh Bird Monitoring Protocol (Conway 2011) and A Unified Strategy for Monitoring Changes in

Abundance of Terrestrial Birds Associated with North American Tidal Marshes (Conway and Droege

2006). The project area and the reference site will be divided into 16-hectare or 400 meter grids. Point-

count surveys will be placed within the center of each grid. Surveys will begin 30 minutes prior to

sunrise and up to three hours after sunrise. Surveys will consist of three parts: 1) a 5-minute passive

listening period during which all species seen or heard are detected 2) a 5-minute passive listening

period during which focal marsh bird detections and estimated distances are recorded 3) playback

recordings of secretive marsh birds, including Sora, Virginia rail, American bittern, American coot, and

pied-billed grebe. Digital vocalizations of each secretive species will be broadcast for 30 seconds,

followed by 30 seconds of silence. We will survey each marsh (references and Qwuloolt) every other

month during the non-breeding season (July 1st – May 14

th) and three times over the course of the

breeding season (May 15st - June 30

th). Surveys will occur during the first week following high tide

because of increased detectability of salt marsh passerines that occurs at this time. Time permitting, we

will also sample at low tides. In addition to using the standardized methods for recording marsh bird use,

we will collect the following information at each point: Tidal stage, moon phase, water depth, salinity,

and current or ongoing management actions at the site.


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Table 1. Focal marsh bird species for bird count surveys, Snohomish River estuary, Marysville, WA, USA.

Focal species

green heron (Butorides virescens)

great blue heron (Ardea herodias)

northern harrier (Circus cyaneus)

osprey (Pandion haliaetus)

Sora (Porzana carolina)

Virginia rail (Rallus limicola)

American bittern (Botaurus lentiginosus)

Wilson’s Snipe (Gallinago delicata)

American coot (Fulica americana)

pied-billed grebe (Podilymbus podiceps)

Hydrology

Water column sampling using Seabird

19plusV2 CTD profilers during key

flow and tide stages (e.g., spring and

neap tide series; high and low tide

stages; and high, average, and low flow

conditions) at previously sampled

stations in the mainstem and Ebey

Slough, as well as expansion into

previously omitted sections of

Steamboat, Union, and Ebey Sloughs

(Figure 1). Once on site, CTD units

will be deployed alongside the boat and

lowered at approximately 1m/sec until

the unit contacts the bottom and

retrieved at the same speed. Data will

be downloaded after each sampling

event and stored in digital format in

multiple locations.

Temperature, salinity, and water level

will be continuously monitored at 12

sites throughout the estuary using

Solinst Model 3001 LTC Levelogger

Junior dataloggers. Loggers will be

placed in 3” PVC well pipe and

secured to existing pilings at each site.

The top of each well will be surveyed

using real-time kinematic (RTK) GPS

to provide for corrections/comparisons

Figure 1. Locations for CTD casts (red dots) and continuous

temperature, salinity, and water level loggers (green dots) in the

Snohomish River estuary.


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among sites. Data will be recorded at 10 minute intervals and individual loggers will be downloaded and

recalibrated every 60 days.

Sediment Dynamics

The RSET and SET-MH developed by the USGS fills the critical need for precise and easily replicable

local surface elevation change measurements. The RSET-MH was developed to quantify the surface and

shallow subsurface processes contributing to wetland surface elevation change. An RSET involves very

simple technology; it consists of a benchmark rod driven through the soil profile to resistance (typically

10-25 m depth), and a portable horizontal arm that is attached at a fixed point to measure the distance to

the substrate surface, using vertical pins. Installation, maintenance and data collection require minor

training.

Total surface height measurements have confidence intervals of ±1.3 mm, a figure well within the

annual rate of eustatic SLR. RSETs are the only tool that can capture surface elevation change with this

precision. RSET data are usually complemented with shallow accretionary monitoring using artificial

soil marker horizons (MH) typically made of feldspar, which simultaneously quantify rates of vertical

surface accretion (i.e., sediment deposition). The complete RSET MH setup provides net surface

elevation change above the benchmark depth; moreover, as it has been repeatedly shown that vertical

accretion is not a valid substitute for surface elevation change, the complete setup is necessary to

identify the contribution of surface and shallow subsurface processes to surface elevation change at a

specific site. Repeated measurements allow chronicling of net surface elevation change, which can be

integrated with region-specific relative SLR (tide gauge data) to determine whether the surface elevation

has kept pace with SLR over that time period.

RSET data can inform assessments of wetland vulnerability to SLR and bolster SLR wetland models to

support science-based policy. RSET networks will contribute to increased confidence in identifying

coastal wetland vulnerability, to more informed science based policy, and to improved accuracy and

efficiency of coastal conservation, mitigation, and adaptation responses.

The USGS has established protocols for the installation of the RSET/MH technology and will provide

training sessions for this effort. USGS personnel will be in the field during installation to ensure quality

control. USGS also has established protocols and templates for data collection and analysis and will

provide these templates and training for this effort (Boumans 1993). USGS and WWU will provide this

technical assistance as an in-kind effort for this project.

SAMPLE HANDLING AND CUSTODY All fish samples collected during beach seining will be immediately placed on ice and taken back to the

NOAA NWFSC Mukilteo Research station for processing and archival by contracted NOAA staff.

Individuals collected at a given site will be labeled accordingly with site information, date of collection,

and the total number and species of individuals included in each sample. Once returned to the lab each

individual will be given a unique sample number before being measured and weighed. After initial

measurements otoliths and stomachs will be extracted and archived for later analysis. Otoliths will be

removed and placed dry into 20mL scintillation vials labeled with sample number, site name, date of

collection and individual lengths and weights. Individual stomachs will be removed and placed into

20mL scintillation vials and fixed with a neutral buffered formalin solution for preservation of gut


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contents until analysis. Stomach vials will be labeled with sample number, site name, date of collection

and individual lengths and weights. Once otoliths and stomachs are removed from each sample,

carcasses will be placed in individual Ziploc bags labeled with sample number, site name, date of

collection and individual lengths and weights and immediately frozen and archived for stable isotope or

genetic analysis. All sample handling, transporting, and processing will be performed by field collection

staff responsible for collecting the respective samples.

ANALYTICAL METHODS Fish abundance and bird count data will be assembled as a site x species matrix and analyzed using

multivariate statistical techniques with the PRIMER statistical package (Clarke 1993). Abundance and

count data will likely be transformed to reduce potential bias caused by extremely large values. All

analyses will be conducted on resemblance matrices constructed using the Bray-Curtis similarity

coefficient. Species richness for bird count data will be computed using SPECRICH, a program that

computes total number of species from empirical species abundance distribution data, based on methods

described by Burnham and Overton (1979). Detection probability will be calculated for all focal marsh bird

species using the program DISTANCE.

QUALITY CONTROL All methods for data collection will be cross-validated with referenced sources. In addition all field

instruments will be calibrated throughout the sampling period according to the methods outlined by

specific manufacturers. Comments will also be added to database describing specific deviations in

quality control. During data analysis, outliers will be defined as data points surpassing 95% confidence

intervals. Outliers will not be discarded, but will be flagged for further consideration.

INSTRUMENT/EQUIPMENT TESTING, INSPECTION AND MAINTENANCE

Field Instruments

Field instruments that will be used to monitor system-wide hydrology (temperature, salinity, water level)

will be maintained in accordance with the manufacturer’s manual. Field instrument operation and

maintenance logbooks will be maintained for the project. Field instruments will be tested annually by

manufacturer.

INSTRUMENT/EQUIPMENT CALIBRATION AND FREQUENCY

Field Instruments

Field instruments will be calibrated before deployment and on site after every download event (every 2

months) in accordance with methods recommended by the manufacturer using the proprietary software.

Records of calibration will be stored digitally on field computers after every calibration event.

INSPECTION/ACCEPTANCE OF CONSUMABLE SUPPLIES Consumable supplies in the field and laboratory will consist of sample bags/containers, sampling

supplies, reagents and SRM’s. The quality of SRM’s and other consumable supplies such as sample

bottles used for this project should be documented by the supplier and certificates should be available to

EPA on request.


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NON-DIRECT MEASUREMENTS (SECONDARY DATA) All secondary data pertains to GIS-related work related to survey design. Site selection for fish sampling

and hydrology was based on secondary data as outlined in Table 3.

Table 3. Secondary data used in survey design.

Data Source Layer URL

LiDAR DEM and

RGB Orthophotos

Watershed

Sciences

Multiple http://pugetsoundlidar.org/

Hyrdography

1:100,000

NHD NHDplus http://www.horizon-systems.com/nhdplus/

DATA MANAGEMENT Sample collections for each sample type at each site will be recorded in Filemaker Pro electronic

databases, and samples will be cross-referenced within this database by site and date. Data will be

handled by different people according to Table 4. All data will be backed up immediately after

downloading from instruments or after acquisition.

Table 4. Data management strategy for each type of measurement

Metric Procedure Person responsible

Hydrology Sample acquisition, data download,

archiving, analysis

Jason Hall

Fish

Sample acquisition

Data acquisition, archiving, analysis

Casey Rice, Joshua

Chamberlin

Birds Sample acquisition


Jason Schilling

Sediment Dynamics

Sample acquisition


Todd Zackey

5. ASSESSMENTS AND RESPONSE ACTIONS

Quality assurance (QA) assessments will be conducted during the course of this project. Given the short

time frame, only one assessment is planned before completion of the project. The quality assurance

assessment performed during this project may include the following:

1) Oversight of field sampling activities.

2) Oversight of sample handling and chain-of-custody procedures.

Quality assurance assessments (Technical System Audit or Quality System Review) will be conducted

by the EPA Region 10 Puget Sound Team including the QA Manager or designee. If, for any reason, the

schedules or procedures above cannot be followed, the project manager shall complete Attachment 1 –


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Sample Alteration Form (SAF). The SAF should be reviewed and approved by the QAO. The

laboratory should be given a copy of the QAO approved SAF for reference and project file.

Corrective action procedures that might be implemented from the assessments or detection of

problems/obstacles encountered during project implementations will be resolved and documented in

Attachment 2 – Corrective Action Form.

6. DATA VALIDATION AND USABILITY VERIFICATION AND VALIDATION METHODS Data Verification

Data verification is a consistent and systematic process that determines whether the data have been

collected in accordance with the QAPP. Data verification will include a review of the findings of all QA

assessment activities including:

1) Field Collection Procedures

2) Sample Labeling Methods

3) Chain-of-Custody Procedures

If any deviations are identified, the potential impact of those deviations on the reliability of the data will

be assessed, and the information will be provided to the project manager.

Data Validation

Data validation is an evaluation of the technical usability of the verified data with respect to the planned

objectives of the project. Data validation consists of evaluation of all individual samples collected and

analyzed to determine if the results are within acceptable limits. Quantitative or qualitative limits of

acceptability are defined for precision, accuracy, representativeness, comparability, and completeness.

RECONCILIATION WITH USER REQUIREMENTS

Anticipated Outputs and Outcomes

Outputs. The proposed work will assess the existing condition of several biotic and abiotic components

of the estuarine ecosystem as a response to ongoing restoration efforts and climate change. Our goal is to

monitor the present condition of the estuary as it relates to species composition and abundance (fish &

birds), hydrology, and sediment dynamics and to synthesize the data and compare the results to pre-

restoration conditions. System-wide monitoring of fish use and hydrology will enable us to determine

patterns of spatial and temporal variation throughout the estuary and help provide context and inform

future management decisions. Bird counts and sediment dynamics within the project site and at adjacent

reference sites will provide critical information on pre-restoration conditions and help to create a

hypothesized trajectory for conditions as they respond to restoration.


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Outcomes. These outputs relate to several important short-term and long-term outcomes. Our results will

feed directly into the comprehensive adaptive management plan developed for the Qwuloolt restoration

project (Rice et al. 2011). Continued fish sampling and hydrology data collection, expanded bird counts,

and additional sediment dynamics data will supplement the existing pre-breach dataset and ensure

Results from the system-wide monitoring component of the proposed work will not only provide context

for past and present restoration projects (Qwuloolt, Union Slough) but may also be used to inform future

management decisions regarding restoration projects by providing critical data for prioritizing future

sites throughout the estuary.

7. REFERENCES

Audubon Washington. 2009. Birds and Climate Change: Washington’s Birds at Risk. Audubon

Washington. Seattle, WA.

Bartz, K.K., K.M. Lagueux, M.D. Scheuerell, T. Beechie, A.D. Haas, and M.H. Ruckelshaus. 2006.

Canadian Journal of Fisheries and Aquatic Sciences. 63:1578–1595.

Beamer, E., A. McBride, C. Greene, R. Henderson, G. Hood, K. Wolf, K. Larsen, C. Rice, and K. Fresh.

2005. Delta and Nearshore Restoration for the Recovery of Wild Skagit River

Boumans, R., and J.W. Day, Jr. 1993. High precision measurements of sediment elevation in shallow

coastal areas using a sedimentation-erosion table. Estuaries 16:375-380.

City of Everett, 2001. Salmon Overlay to the Snohomish Estuary Wetland Integration Plan. 2001. City

of Everett Department of Planning and Community Development, Everett, WA.

Conway, C. J., and S. Droege. 2006. A Unified Strategy for Monitoring Changes in Abundance

of Birds Associated with North American Tidal Marshes. Studies in Avian Biology

32:382-397.

Conway, C. J. 2011. Standardized North American Marsh Bird Monitoring

Protocol. Waterbirds 34:319-346.

Chinook Salmon: Linking Estuary Restoration to Wild Chinook Salmon Populations. Appendix D of the

Skagit Chinook Recovery Plan, Skagit River System Cooperative, LaConner, Washington.

Cowardin, L.M., V. Carter, F.C. Golet, and E.T. LaRoe. 1979. Classification of wetlands and deepwater

habitats of the United States. U.S. Fish and Wildlife Service. FWS/OBS-79-31.

Greene, C. M., and E. M. Beamer. 2009. Monitoring of population responses by Skagit River Chinook

salmon to estuary restoration. Intensively Monitored Watershed Program Annual Report.


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Guntenspergen, G. 2012. Personal communication regarding integration of Snohomish estuary sites with

two ongoing USGS studies: 1) Downscaling climate change models to local site conditions: effects of

sea-level rise and extreme events to U.S. Pacific Coast wetland habitats. 2) Forecasting Coastal Marsh

Responses to Climate Change and Rising Sea Levels: Potential Impacts and Adaptations.

Haas, A., and B. D. Collins. 2001. A Historical Analysis of Habitat Alteration in the Snohomish River

Valley, Washington since the mid-19th Century: Implications for Chinook and Coho Salmon. Report for

Snohomish County.

Johnson, G. E., H. L. Diefenderfer, A. B. Borde, E. M. Dawley, B. D. Ebberts, D. A. Putman, G. C.

Roegner, M. Russell, J. R. Skalski, R. M. Thom, and J. Vavrinec III. 2008. Evaluating Cumulative

Ecosystem Response to Restoration Projects in the Columbia River Estuary, Annual Report 2007.

PNNL-17437. Pacific Northwest National Laboratory, Richland, WA.

Kairis, P. and J.M. Rybczyk. 2010. A Spatially Explicit Relative Elevation Model for Padilla Bay, WA.

Ecological Modeling. 221: 1005 -1016.

Khangaonkar T., Yang, Z., Kim, T., and Roberts, M. (2011) Tidally averaged circulation in Puget Sound

sub-basins: comparison of historical data, analytical model, and numerical model. Estuarine, Coastal,

and Shelf Science, 93(4):305–319.

Neckles, H.A., Dionne, M., Burdick, D.M., Roman, C.T., Buchsbaum, R. & Hutchins, E. (2002). A

monitoring protocol to assess tidal restoration of salt marshes on local and regional

scales. Restoration Ecology, 10, 556–563.

Puget Sound Partnership. 2012. The action agenda for the Puget Sound (draft). Puget Sound Partnership,

Tacoma, WA.

Puget Sound Recovery Implementation Technical Team (RITT). 2012. A Common Framework for

Monitoring the Recovery of Puget Sound Chinook Salmon and Adapting Salmon Recovery Plans. Draft

NOAA Technical Memorandum. NOAA, Northwest Fisheries Science Center, Seattle, WA.

Rice, C. A. and eleven others. 2011. Monitoring Plan for the Qwuloolt Restoration Project. 70p.

Background, scheduling, and cost estimates for three years pre-, and ten years post-levee breach

monitoring.

Rowse, M., and K. L. Fresh. 2003. Juvenile salmonid utilization of the Snohomish River estuary, Puget

Sound.in T. W. Droscher and D. A. Fraser, editors. Proceedings of the 2003 Georgia Basin/Puget Sound

Research Conference (2003).

Snohomish Basin Salmon Recovery Forum. 2005. Snohomish River Basin Salmon Conservation Plan.

Snohomish County Department of Public Works, Surface Water Management Division, Everett, WA.

Washington Department of Fish and Wildlife. 2005. Comprehensive Wildlife Conservation Strategy.

Olympia, WA. 788 p.


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Wentworth-Davis, T. 2011. Current and Future Bird Use of the Project Area. Appendix D in Smith

Island Restoration Project. Snohomish County Department of Public Works, Everett, WA.

Sprecher, S. W. 2000. Installing monitoring wells/piezometers in wetlands, WRAP Technical Notes

Collection (ERDC TN-WRAP-00-02), U.S. Army Engineer Research and Development Center,

Vicksburg, MS. www.wes.army.mil/el/wrap

U.S. EPA. 2002. Methods for Evaluating Wetland Condition: Biological Assessment Methods

for Birds. Office of Water, U.S. Environmental Protection Agency, Washington, DC. EPA-822-R-

02-023.

Zhaoqing, Yang, and T. Khangaonkar. 2008. Modeling of salt intrusion, intertidal mixing, and

circulation in a braided estuary. Journal of Coastal Research. 171-180.

http://www.wes.army.mil/el/wrap

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