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UNIT 3

Toolbox of Assessment Methods

APPENDIX A

Habitat Characterization

CONTENTS

The Qualitative Habitat Evaluation Index (QHEI) (OEPA 1989) ................................................643 Geographical Information ....................................................................................................643 Riffle and Run Habitats........................................................................................................645 Pool and Glide Habitats .......................................................................................................646 Computing the Total QHEI Score........................................................................................650 Stream Map ..........................................................................................................................652

The USEPA Habitat Assessment for the Rapid Bioassessment Protocols (EPA 1999)...............652 Water Quality........................................................................................................................656 Physical Characterization .....................................................................................................658 Procedure for Performing the Habitat Assessment..............................................................662 Quality Assurance Procedures..............................................................................................662

References ......................................................................................................................................662

While more advanced habitat quantification methods are available (see Chapters 5 and 6), rapid methods have proven to be quite useful. Two of the more popular and similar approaches for assessing the habitat of streams and rivers are described below. These methods are not particularly useful for large rivers, lakes, or coastal areas. Habitat effects may be qualitatively evaluated using methods of the Ohio EPA (OEPA 1989) or the USEPA Rapid Bioassessment Protocol (EPA 1999), both of which are described in this appendix. The Qualitative Habitat Evaluation Index (QHEI) was issued by the OEPA for fish sampling, but it may be also used in any type of stream survey.

THE QUALITATIVE HABITAT EVALUATION INDEX (QHEI) (OEPA 1989)

A general evaluation of macrohabitat is made while sampling each location using the Ohio EPA Site Description Sheet — Fish (Figures A.1 and A.2). This form is used to tabulate data and information for calculating the Qualitative Habitat Evaluation Index (QHEI). The following guidance should be used when completing the site evaluation form.

Geographical Information

1. Stream, River Mile (RM), Date The official stream name may be found in the State Gazetteer of streams or on USGS 7.5 minute topographic maps.

643

644 STORMWATER EFFECTS HANDBOOK

Figure A.1 Front side of the Ohio EPA Site Description Sheet for the Qualitative Habitat Evaluation Index (QHEI). (From Ohio Environmental Protection Agency. The Qualitative Habitat Evaluation Index (QHEI): Rationale, Methods, and Application. Ecological Assessment Section, Ohio Environmental Protection Agency, Columbus, OH. 1989.)

2. Specific Location A brief description of the sampling location should include proximity to a local landmark such as a bridge, road, discharge outfall, railroad crossing, park, tributary, dam, etc.

3. Field Sampling Crew The field crew involved with the sampling is noted on the sheet, with the person who filled out the sheet listed first.

HABITAT CHARACTERIZATION 645

Figure A.2 Reverse side of the Ohio EPA Site Description Sheet for evaluating the geographical and physical characteristics of fish sampling locations. This is used to record additional information about the sampling site and adjacent area. (From Ohio Environmental Protection Agency). The Qualitative Habitat Evaluation Index (QHEI): Rationale, Methods, and Application. Ecological Assessment Section, Ohio Environmental Protection Agency, Columbus, OH. 1989.)

4. Habitat Characteristics: QHEI Metrics The Qualitative Habitat Evaluation Index (QHEI) is a physical habitat index designed to provide an empirical, quantified evaluation of the general lotic macrohabitat characteristics that are important to fish communities. The QHEI is composed of six principal metrics each of which is described below. The maximum possible QHEI site score is 100. Each of the metrics is scored individually and then summed to provide the total QHEI site score. This is completed at least once for each sampling site during each year of sampling. An exception to this convention is when substantial changes to the macrohabitat have occurred between sampling passes. Standardized definitions for pool, run, and riffle habitats, for which a variety of existing definitions and perceptions exist, are essential for using the QHEI accurately. It is recommended that this reference also be consulted prior to scoring individual sites.

Riffle and Run Habitats

Riffle — areas of the stream with fast current and shallow depth; the water surface is visibly broken.

Run — areas of the stream that have a rapid, nonturbulent flow; runs are deeper than riffles, with a faster current velocity than pools, and are generally located downstream from riffles where the stream narrows; the stream bed is often flat beneath a run and the water surface is not visibly broken.


Pool and Glide Habitats

Pool — an area of the stream with slow current velocity and a depth greater than riffle and run areas; the stream bed is often concave and stream width frequently is the greatest; the water surface slope is nearly zero. If a pool or glide has a maximum depth of less than 20 cm, it is deemed to have lost its functionality and the metric is scored a 0.

Glide — an area common to most modified stream channels that does not have distinguishable pool, run, and riffle habitats; the current and flow are similar to that of a canal; the water surface gradient is nearly zero.

The following is a description of each of the six QHEI metrics and the individual metric components. Guidelines on how to score each are presented. Generally, metrics are scored by checking boxes. In certain cases, the biologist completing the QHEI sheet may interpret a habitat characteristic as being intermediate between the possible choices; in cases where this is allowed (denoted by the term “Double-Checking”), two boxes may be checked and their scores averaged.

Metric 1: Substrate

This metric includes two components, substrate type and substrate quality.

Substrate Type — Check the two most common substrate types in the stream reach. If one substrate type predominates (greater than approximately 75 to 80%) of the bottom area or is clearly the most functionally predominant substrate), then this substrate type should be checked twice. DO NOT CHECK MORE THAN TWO BOXES. Note the category for artificial substrates. Spaces are provided to note the presence (by check marks, or estimates of %, if time allows) of all substrate types present in pools and riffles that each comprise at least 5% of the site (i.e., they occur in sufficient quantity to support species that may commonly be associated with the habitat type). This section must be filled out completely to permit future analyses of this metric. If there are more than four substrate types in the zone that are present in greater than approximately 5% of the sampling area, check the appropriate box.

Substrate Quality — Substrate origin refers to the “parent” material that the stream substrate is derived from. Check ONE box under the substrate origin column unless the parent material is from multiple sources (e.g., limestone and tills). Embeddedness is the degree to which cobble, gravel, and boulder substrates are surrounded, impacted in, or covered by fine materials (sand and silt). Substrates should be considered embedded if >50% of surface of the substrates is embedded in fine material. Embedded substrates cannot be easily dislodged. This also includes substrates that are concreted or “armor-plated.” Naturally sandy streams are not considered embedded; however, a sand-predominated stream that is the result of anthropogenic activities that have buried the natural coarse substrates is considered embedded. Boxes are checked for extensiveness (area of sampling zone) of the embedded substrates as follows: Extensive: >75% of site area, Moderate: 50 to 75%, Sparse: 25 to 50%, Low: <25%.

Silt Cover — the extent to which substrates are covered by a silt layer (i.e., more than 1 inch thick). Silt Heavy means that nearly all of the stream bottom is layered with a deep covering of silt. Moderate includes extensive coverings of silts, but with some areas of cleaner substrate (e.g., riffles). Normal silt cover includes areas where silt is deposited in small amounts along the stream margin or is present as a “dusting” that appears to have little functional significance. If substrates are exceptionally clean, the Silt Free box should be checked.


Substrate types are defined as:

a. Bedrock — solid rock forming a continuous surface. b. Boulder — rounded stones over 250 mm in diameter (10 in) or large “slabs” more than 256 mm

in length (boulder slabs). c. Cobble — stones from 64 to 256 mm (21/2 to 10 in) in diameter. d. Gravel — mixture of rounded coarse material from 2 to 64 mm (0.8 to 21/2 in) in diameter. e. Sand — materials 0.06 to 2.0 mm in diameter, gritty texture when rubbed between fingers. f. Silt — 0.004 to 0.06 mm in diameter; generally this is fine material which feels “greasy” when

rubbed between fingers. g. Hardpan — particles less than 0.004 mm in diameter, usually clay, which form a dense, gummy

surface that is difficult to penetrate. h. Marl — calcium carbonate; usually grayish-white; often contains fragments of mollusc shells. i. Detritus — dead, unconsolidated organic material covering the bottom, which could include sticks,

wood, and other partially or undecayed coarse plant material. j. Muck — black, fine, flocculent, completely decomposed organic matter (does not include sewage

sludge). k. Artificial — substrates such as rock baskets, gabions, bricks, trash, concrete, etc., placed in the

stream for reasons OTHER than habitat mitigation.

Sludge is defined as thick layers of organic matter, that is decidedly of human or animal origin. NOTE: SLUDGE THAT ORIGINATES FROM POINT SOURCES IS NOT INCLUDED; THE SUBSTRATE SCORE IS BASED ON THE UNDERLYING MATERIAL.

Substrate Metric Score — Although the theoretical maximum metric score is > 20, the maximum score allowed for the QHEI is limited to 20 points.

Metric 2: In-Stream Cover

This metric consists of in-stream cover type and in-stream cover amount. All of the cover types that are present in amounts greater than approximately 5% of the sampling area (i.e., they occur in sufficient quantity to support species that may commonly be associated with the habitat type) should be checked. Cover should not be counted when it is in areas of the stream with insufficient depth (usually <20 cm) to make it useful. For example, a logjam in 5 cm of water contributes very little if any cover and may be dry at low flow. Other cover types with limited utility in shallow water include undercut banks and overhanging vegetation, boulders, and rootwads. Under amount, one or two boxes may be checked. Extensive cover is that which is present throughout the sampling area, generally greater than about 75% of the stream reach. Cover is moderate when it occurs over 25 to 75% of the sampling area. Cover is sparse when it is present in less than 25% of the stream margins (sparse cover usually exists in one or more isolated patches). Cover is nearly absent when no large patch of any type of cover exists anywhere in the sampling area. This situation is usually found in recently channelized streams or other highly modified reaches (e.g., ship channels). If cover is thought to be intermediate in amount between two categories, check two boxes and average their scores. Cover types include: (1) undercut banks, (2) overhanging vegetation, (3) shallows (in slow water), (4) logs or woody debris, (5) deep pools (>70 cm), (6) oxbows, (7) boulders, (8) aquatic macrophytes, and (9) rootwads (tree roots that extend into stream). Do not check undercut banks AND rootwads unless undercut banks exist along with rootwads as a major component.

Cover Metric Score — Although the theoretical maximum score is >20, the maximum score assigned for the QHEI for the in-stream cover metric is limited to 20 points.


Metric 3: Channel Morphology

This metric emphasizes the quality of the stream channel that relates to the creation and stability of macrohabitat. It includes channel sinuosity (i.e., the degree to which the stream meanders), channel development, channelization, and channel stability. One box under each should be checked unless conditions are considered to be intermediate between two categories; in these cases check two boxes and average their scores.

a. Sinuosity — No sinuosity is a straight channel. Low sinuosity is a channel with only one or two poorly defined outside bends in a sampling reach, or perhaps slight meandering within modified banks. Moderate sinuosity is more than two outside bends, with at least one bend well defined. High sinuosity is more than two or three well-defined outside bends with deep areas outside and shallow areas inside. Sinuosity may be more conceptually described by the ratio of the stream distance between these same two points, taken from a topographic map. Check only one box.

b. Development — This refers to the development of riffle/pool complexes. Poor means riffles are absent, or if present, shallow with sand and fine gravel substrates; pools, if present, are shallow. Glide habitats, if predominant, receive a Poor rating. Fair means riffles are poorly developed or absent; however, pools are more developed with greater variation in depth. Good means better defined riffles present with larger substrates (gravel, rubble, or boulder); pools vary in depth and there is a distinct transition between pools and riffles. Excellent means development is similar to the Good category except the following characteristics must be present: pools must have a maximum depth of >1 m and deep riffles and runs (>0.5 m) must also be present. In streams sampled with wading methods, a sequence of riffles, runs, and pools must occur more than once in a sampling zone. Check one box.

c. Channelization — This refers to anthropogenic channel modifications. Recovered refers to streams that have been channelized in the past, but which have recovered most of their natural channel characteristics. Recovering refers to channelized streams which are still in the process of regaining their former, natural characteristics; however, these habitats are still degraded. This category also applies to those streams, especially in the Huron/Erie Lake Plain ecoregion (NW Ohio), that were channelized long ago and have a riparian border of mature trees, but still have Poor channel characteristics. Recent or No Recovery refers to streams that were recently channelized or those that show no significant recovery of habitats (e.g., drainage ditches, grass lined or rock riprap banks, etc.). The specific type of habitat modification is also checked in the two columns, but not scored.

d. Stability — This refers to channel stability. Artificially stable (concrete) stream channels receive a High score. Even though they are generally a negative influence on fish, the negative effects are related to features other than their stability. Channels with Low stability are usually characterized by fine substrates in riffles that often change location, have unstable and severely eroding banks, and a high bedload that slowly creeps downstream. Channels with Moderate stability are those that appear to maintain stable riffle/pool and channel characteristics, but which exhibit some symptoms of instability, e.g., high bedload, eroding or false banks, or show the effects of wide fluctuations in water level. Channels with High stability have stable banks and substrates, and little or no erosion and bedload.

e. Modifications/Other — Check the appropriate box if impounded, islands present, or leveed (these are not included in the QHEI scoring) as well as the appropriate source of habitat modifications.

The maximum QHEI metric score for Channel Morphology is 20 points.

Metric 4: Riparian Zone and Bank Erosion

This metric emphasizes the quality of the riparian buffer zone and quality of the floodplain vegetation. This includes riparian zone width, floodplain quality, and extent of bank erosion. Each of the three components requires scoring the left and right banks (looking downstream). The average of the left and right banks is taken to derive the component value. One box per bank should be


checked unless conditions are considered to be intermediate between two categories; in these cases check two boxes and average their scores.

a. Width of Floodplain Vegetation — This is the width of the riparian (stream side) vegetation. Width estimates are only done for forest, shrub, swamp, and old field vegetation. Old field refers to a fairly mature successional field that has stable, woody plant growth; this generally does not include weedy urban or industrial lots that often still have high runoff potential. Two boxes, one each for the left and right bank (looking downstream), should be checked and then averaged.

b. Floodplain Quality — The two most predominant floodplain quality types should be checked, one each for the left and right banks (includes urban, residential, etc.), and then averaged. By floodplain we mean the areas immediately outside the riparian zone or greater than 100 ft from the stream, whichever is wider on each side of the stream. These are areas adjacent to the stream that can have direct runoff and erosional effects during normal wet weather. We do not limit it to the riparian zone, and it is much less encompassing than the stream basin.

c. Bank Erosion — The following Streambank Soil Alteration Ratings should be used; check one box for each side of the stream and average the scores. False banks mean banks that are no longer adjacent to the normal flow of the channel but have been moved back into the floodplain, most commonly as a result of livestock trampling.

1. None — stream banks are stable and not being altered by water flows or animals (e.g., livestock) — Score 3.

2. Little — stream banks are stable, but are being lightly altered along the transect line; less than 25% of the stream bank is receiving any kind of stress, and if stress is being received it is very light; less than 25% of the stream bank is false, broken down, or eroding — Score 3.

3. Moderate — stream banks are receiving moderate alteration along the transect line; at least 50% of the stream bank is in a natural stable condition; less than 50% of the stream bank is false, broken down, or eroding; false banks are rated as altered — Score 2.

4. Heavy — stream banks have received major alterations along the transect line; less than 50% of the stream bank is in a stable condition; over 50% of the stream bank is false, broken down, or eroding — Score 1.

5. Severe — stream banks along the transect line are severely altered; less than 25% of the stream bank is in a stable condition; over 75% of the stream bank is false, broken down, or eroding — Score 1.

The maximum score for Riparian Zone and Erosion metric is 10 points.

Metric 5: Pool/Glide and Riffle-Run Quality

This metric emphasizes the quality of the pool, glide, and/or riffle-run habitats. This includes pool depth, overall diversity of current velocities (in pools and riffles), pool morphology, riffle-run depth, riffle-run substrate, and riffle-run substrate quality.

A. POOL/GLIDE QUALITY 1. Maximum depth of pool or glide — check one box only (Score 0 to 6). Pools or glides with

maximum depths of less than 20 cm are considered to have lost their function and the total metric is scored a 0. No other characteristics need be scored in this case.

2. Current Types — check each current type that is present in the stream (including riffles and runs; score — 2 to 4), definitions are: Torrential — extremely turbulent and fast flow with large standing waves; water surface is very

broken with no definable, connected surface; usually limited to gorges and dam spillway tailwaters.

Fast — mostly nonturbulent flow with small standing waves in riffle-run areas; water surface may be partially broken, but there is a visibly connected surface.

Moderate — nonturbulent flow that is detectable and visible (i.e., floating objects are readily transported downstream); water surface is visibly connected.


Slow — water flow is perceptible, but very sluggish. Eddies — small areas of circular current motion usually formed in pools immediately down

stream from riffle-run areas. Interstitial — water flow that is perceptible only in the interstitial spaces between substrate par

ticles in riffle-run areas. Intermittent — no flow is evident anywhere leaving standing pools that are separated by dry areas.

3. Morphology — Check Wide if pools are wider than riffles, Equal if pools and riffles are the same width, and Narrow if the riffles are wider than the pools (Score 0 to 2). If the morphology varies throughout the site, average the types. If the entire stream area (including areas outside of the sampling zone) is pool or riffle, then check riffle = pool.

Although the theoretical maximum score is >12, the maximum score assigned for the QHEI for the Pool Quality metric is limited to 12 points.

B. RIFFLE-RUN QUALITY (score 0 for this metric if no riffles are present) 1. Riffle/Run Depth — Select one box that most closely describes the depth characteristics of the

riffle (Score 0 to 4). If the riffle is generally less than 5 cm in depth, riffles are considered to have lost their function and the entire riffle metric is scored a 0.

2. Riffle/Run Substrate Stability — Select one box from each that best describes the substrate type and stability of the riffle habitats (Score 0 to 2).

3. Riffle/Run Embeddedness — Embeddedness is the degree that cobble, gravel, and boulder substrates are surrounded or covered by fine material (sand, silt). We consider substrates embedded if >50% of the surface of the substrates is embedded in fine material, as these substrates cannot be easily dislodged. This also includes substrates that are concreted. Boxes are checked for extensiveness (riffle area of sampling zone) with embedded substrates: Extensive: >75% of stream area, Moderate: 50 to 75%, Sparse: 25 to 50%, Low: <25%.

The maximum score assigned for the QHEI for the Riffle/Run Quality metric is 8 points.

Metric 6: Map Gradient

Local or map gradient is calculated from USGS 7.5 minute topographic maps by measuring the elevation drop through the sampling area. This is done by measuring the stream length between the first contour line upstream and the first contour line downstream of the sampling site and dividing the distance by the contour interval. If the contour lines are closely “packed,” a minimum distance of at least 1 mile should be used. Some judgment may need to be exercised in certain anomalous areas (e.g., in the vicinity of waterfalls, impounded areas, etc.), and this can be compared to an in-field, visual estimate, which is recorded on the back of the habitat sheet.

Scoring for ranges of stream gradient takes into account the varying influence of gradient with stream size (measured as drainage area in square miles or stream width). Gradient classifications (Table A.1) were modified from Trautman (1981), and scores were assigned, by stream size category, after examining scatterplots of IBI vs. natural log of gradient in ft/mile. Scores are listed in Table A.1.

The maximum QHEI metric score for Gradient is 10 points.

Computing the Total QHEI Score

To compute the total QHEI score, add the components of each metric to obtain the metric scores and then sum the metric scores to obtain the total QHEI score. The QHEI metric scores cannot exceed the Metric Maximum Score indicated below:

Additional Information

Additional information is recorded on the reverse side of the Site Description Sheet (Figure A.2) and is described as follows:


Table A.1 Classification of Stream Gradients for Ohio, Corrected for Stream Size. Scores Were Derived from Plots of IBI vs. the Natural Log of Gradient for Each Stream Size Category

Stream Drainage Width Area Very Low– Moderate– Very

(m) (mi2) Low Low Moderate Moderate High High Higha

0.3–4.7 0–9.2 0–1.0 1.1–5.0 5.1–10.0 10.1–15.0 15.1–20 20.1–30 30.1–40 2 4 6 8 10 10 8

4.8–9.2 9.2–41.6 0–1.0 1.1–3.0 3.1–6.0 6.1–12.0 12.1–18.0 18.0–30 30.1–40 2 4 6 10 10 8 6

9.2–13.8 41.6–103.7 0–1.0 1.1–2.5 2.6–5.0 5.1–7.5 7.6–12.0 12.1–20 20.1–30 2 4 6 8 10 8 6

3.9–30.6 103.7–622.9 0–1.0 1.1–2.0 2.1–4.0 4.1–6.0 6.1–10.0 10.1–15 15.1–25

4 6 8 10 10 8 6 >30.6 > 622.9 — 0–0.5 0.6–1.0 1.1–2.5 2.6–4.0 4.1–9.0 > 9.0

6 8 10 10 10 8

a Any site with a gradient greater than the upper bound of the “very high” gradient classification is assigned a score of 4.

1. Additional Comments/Pollution Impacts — Different types of pollution sources (e.g., wastewater treatment plant, feedlot, industrial discharge, nonpoint source inputs) are noted with their proximity (in 0.1-mile increments) to the sampling site; any evidence of litter, either in-stream or on the stream bank, is also noted.

2. Sampling Gear/Distance Sampled — The type of fish sampling gear used during each pass is specified, and any variation in sampling procedures is noted (e.g., sampler type A specifies sampling along one shoreline of 0.5 km, but due to local restriction, sampling may be performed on both shorelines to accumulate 0.5 km); the total sampling distance in kilometers for each sampling site for each pass is recorded.

3. Water Clarity — The following descriptions can be used as a guide: a. Clear — bottom is clearly visible (if shallow enough), and the water contains no apparent color

or staining. b. Stained — usually a brownish (or other) color to the water; the bottom may be visible in

shallow areas. c. Turbid — bottom seldom visible at more than a few inches; caused by suspended sediment particles.

The apparent source of stained (e.g., tannic acid, leaf decay, etc.) and turbid (e.g., runoff [clay/silt], algae/diatoms, sewage, etc.) water may be specified under additional comments.

4. Water Stage — This is the general water level of the stream during each pass; suggested descriptors are: a) flood, b) high, c) elevated, d) normal, e) low, and f) interstitial. (Note: sampling should not be conducted during flood or high flows.)

5. Canopy — This is the percentage of the sampling site that is not covered or shaded by woody bank vegetation. In wide streams and rivers, this determination should be made along both sides of the river or stream (i.e., the percent of the sampling path that is open).

6. Gradient — Check the box that best describes the gradient at the site. This will be used to check the accuracy of gradients taken from topographic maps.

7. Field Crew — The names of all individuals involved with the sampling/site description at each site are included.

8. Photographs — The number of each photograph taken is recorded; the subject of the photograph is briefly described.

9. Stream Measurements (optional) — When measuring the individual sampling sites, length, width, and average and maximum depth information should be recorded; each measurement should be recorded as either a riffle, run, or pool or glide by placing an X in the correct box to the right of where measurements are recorded (Figure A.2); see the introduction for definitions of riffles, runs, etc.

The number of width measurements is left to the discretion of the field crew leader. Short riffles may require only one or two width measurements, while long pools will probably require more,


depending on the degree of variation that exists in the stream’s width. Depth measurements should be made in association with individual width measurements. Depths should be taken at the stream margins and various points across the stream. Up to nine depth measurements may be taken, depending on the variability in the stream bottom. Maximum depth is the deepest spot in the stream section sampled. One purpose of this information is to calculate pool volume.

10. Stream Diagram — Cross sections: Two or three cross sections of the stream are drawn to provide information on features of the stream bank, stream bottom, stream channel, and floodplain. Channel — The cross section containing the stream that is distinct from the surrounding area due

to breaks in the general slope of the land, lack of terrestrial vegetation, and changes in the composition of the substrate materials. The channel is made up of stream banks and stream bottoms.

Banks — The portion of the channel cross section that tends to restrict lateral movement of water. The banks often have a slope steeper than 45° and exhibit a distinct break in slope from the stream bottom. Also, an obvious change in substrate materials is a reliable delineation of the bank.

Stream Bottom — The portion of the channel cross section not classified as bank. The bottom is usually composed of stream sediments or water transported debris and may be covered by rooted or clinging aquatic vegetation. In some geologic formations, the stream bottom may consist of bedrock rather than sediments.

Floodplain — The area adjacent to the channel that is seasonally submerged under water. Usually the floodplain is a low area covered by various types of riparian vegetation.

Stream Map

The entire sampling zone is sketched in the area provided. Important physical features are noted on the map with standard symbols used where possible. The sampling path taken is described, along with any other pertinent information.

THE USEPA HABITAT ASSESSMENT FOR THE RAPID BIOASSESSMENT PROTOCOLS (EPA 1999)

Rosgen (1985, 1994, 1996) presented a stream and river classification system that is founded on the premise that dynamically stable stream channels have a morphology that provides appropriate distribution of flow energy during storm events. Further, he identifies eight major variables that affect the stability of channel morphology, but are not mutually independent: channel width, channel depth, flow velocity, discharge, channel slope, roughness of channel materials, sediment load, and sediment particle size distribution. When streams have one of these characteristics altered, some of their capability to dissipate energy properly is lost (Leopold et al. 1964; Rosgen 1985) and will result in accelerated rates of channel erosion. Some of the habitat structural components that function to dissipate flow energy are sinuosity, roughness of bed and bank materials, presence of point bars (slope is an important characteristic), vegetative conditions of stream banks and the riparian zone, condition of the floodplain (accessibility from bank, overflow, and size are important characteristics).

Measurement of these parameters or characteristics serves to stratify and place streams into distinct classifications. However, none of these habitat classification techniques attempts to differentiate the quality of the habitat and the ability of the habitat to support the optimal biological condition of the region. Much of our understanding of habitat relationships in streams has emerged from comparative studies that describe statistical relationships between habitat variables and abundance of biota (Hawkins et al. 1993). A rapid and qualitative habitat assessment approach has been developed to describe the overall quality of the physical habitat (Ball 1982; Ohio EPA 1987; Plafkin


et al. 1989; Barbour and Stribling 1991, 1994; Rankin 1991, 1995). For a more detailed guidance, please refer to the original document (USEPA 1999, www.epa.gov/owow/monitoring/rbp/).

The habitat assessment matrix developed for the Rapid Bioassessment Protocols (RBPs) in Plafkin et al. (1989) were originally based on the Stream Classification Guidelines for Wisconsin developed by Ball (1982) and “Methods of Evaluating Stream, Riparian, and Biotic Conditions” developed by Platts et al. (1983). Barbour and Stribling (1991, 1994) modified the habitat assessment approach originally developed for the RBPs to include additional assessment parameters for high-gradient streams and a more appropriate parameter set for low-gradient streams. All parameters are evaluated and rated on a numerical scale of 0 to 20 (highest) for each sampling reach. The ratings are then totaled and compared to a reference condition to provide a final habitat ranking. Scores increase as habitat quality increases. To ensure consistency in the evaluation procedure, descriptions of the physical parameters and relative criteria are included in the rating form (Figures A.3 through A.8).

A biologist who is well versed in the ecology and zoogeography of the region can generally recognize optimal habitat structure as it relates to the biological community. The ability to accurately assess the quality of the physical habitat structure using a visual-based approach depends on several factors: the parameters selected to represent the various features of habitat structure need to be relevant and clearly defined; a continuum of conditions for each parameter must exist that can be characterized from the optimum for the region or stream type under study to the poorest situation reflecting substantial alteration due to anthropogenic activities; the judgment criteria for the attributes of each parameter should minimize subjectivity through either quantitative measurements or specific categorical choices, in which the investigators are experienced or adequately trained, for stream assessments in the region under study (Hannaford et al. 1997); adequate documentation and ongoing training must be maintained to evaluate and correct errors resulting in outliers and aberrant assessments.

Habitat evaluations are first made on in-stream habitat, followed by channel morphology, bank structural features, and riparian vegetation. Generally, a single, comprehensive assessment is made that incorporates features of the entire sampling reach as well as selected features of the catchment. Additional assessments may be made on neighboring reaches to provide a broader evaluation of habitat quality for the stream ecosystem. The actual habitat assessment process involves rating the 10 parameters as optimal, suboptimal, marginal, or poor, based on the criteria included on the Habitat Assessment Field Data Sheets. Some state programs, such as Florida Department of Environmental Protection (DEP) (1996) and Mid-Atlantic Coastal Streams Workgroup (MACS) (1996) have adapted this approach using somewhat fewer and different parameters.

Reference conditions are used to scale the assessment to the “best attainable” situation. This approach is critical to the assessment because stream characteristics will vary dramatically across different regions (Barbour and Stribling 1991). The ratio between the score for the test station and the score for the reference condition provides a percent comparability measure for each station. The station of interest is then classified on the basis of its similarity to expected conditions (reference condition), and its apparent potential to support an acceptable level of biological health. Use of a percent comparability evaluation allows for regional and stream-size differences which affect flow or velocity, substrate, and channel morphology. Some regions are characterized by streams having a low channel gradient, such as coastal plains or prairie regions.

Other habitat assessment approaches or a more rigorously quantitative approach to measuring the habitat parameters may be used (see Klemm and Lazorchak 1994; Kaufmann and Robison 1994; Meador et al. 1993). However, holistic and rapid assessment of a wide variety of habitat attributes along with other types of data is critical if physical measurements are to be used to best advantage in interpreting biological data.

A generic habitat assessment approach based on visual observation can be separated into two basic approaches — one designed for high-gradient streams, and one designed for low-gradient streams. High-gradient or riffle/run prevalent streams are those in moderate- to high-gradient landscapes. Natural high-gradient streams have substrates primarily composed of coarse sediment particles


Figure A.3 For use in Rapid Bioassessment Protocols. (From EPA. Rapid Bioassessment Protocols for Use in Wadeable Streams and Rivers: Periphyton, Benthic Macroinvertebrates and Fish. Office of Water, U.S. Environmental Protection Agency, Washington, D.C. EPA 841/B-99/002. 1999.)

(i.e., gravel or larger) or frequent coarse particulate aggregations along stream reaches. Low-gradient or glide/pool prevalent streams are those in low- to moderate-gradient landscapes. Natural low-gradient streams have substrates of fine sediment or infrequent aggregations of more coarse (gravel or larger) sediment particles along stream reaches. The entire sampling reach is evaluated for each parameter. A brief set of decision criteria is given for each parameter corresponding to each of the four categories, reflecting a continuum of conditions on the field sheet (optimal, suboptimal, marginal, and poor).


Figure A.4 For use in Rapid Bioassessment Protocols. (From EPA. Rapid Bioassessment Protocols for Use in Wadeable Streams and Rivers: Periphyton, Benthic Macroinvertebrates and Fish. Office of Water, U.S. Environmental Protection Agency, Washington, D.C. EPA 841/B-99/002. 1999.)

Use of a percent comparability evaluation allows for regional and stream-size differences that affect flow or velocity, substrate, and channel morphology. Some regions are characterized by streams having a low channel gradient. Such streams are typically shallower, have a greater pool/riffle or run/bend ratio, and have a less stable substrate than streams with a steep channel gradient. Although some low-gradient streams do not provide the diversity of habitat or fauna afforded by steeper-


Figure A.5 For use with Rapid Bioassessment Protocols. (From EPA. Rapid Bioassessment Protocols for Use in Wadeable Streams and Rivers: Periphyton, Benthic Macroinvertebrates and Fish. Office of Water, U.S. Environmental Protection Agency, Washington, D.C. EPA 841/B-99/002. 1999.)

gradient streams, they are characteristic of certain regions. Using the approach presented here, these streams may be evaluated relative to other low-gradient streams (USEPA 1989).

Assessment Category Percent of Comparability Comparable to reference ≥90% Supporting 75–88% Partially supporting 60–73% Nonsupporting ≤58%

Water Quality

Information requested in this section is standard to many aquatic studies and allows for some comparison between sites. Additionally, conditions that may significantly affect aquatic biota are



documented. Documentation of recent and current weather conditions is important because of the potential impact that weather may have on water quality. To complete this phase of the bioassessment, a photograph may be helpful in identifying station location and documenting habitat conditions. Any observations or data not requested but deemed important by the field observer should be recorded. This section is identical for all protocols, and the specific data requested are described below:

Temperature (C), Dissolved Oxygen, pH, Conductivity — Measure and record values for each of the water quality parameters indicated, using the appropriate calibrated water quality instrument(s). Note the type of instrument and unit number used.



Stream Type — Note the appropriate stream designation according to state water quality standards. Water Odors — Note those odors described (or include any other odors not listed) that are associated

with the water in the sampling area. Water Surface Oils — Note the term that best describes the relative amount of any oils present on the

water surface. Turbidity — Note the term which, based upon visual observation, best describes the amount of material

suspended in the water column.

Physical Characterization

Physical characterization parameters include estimations of general land use and physical stream characteristics such as width, depth, flow, and substrate. The evaluation begins with the riparian zone (stream bank and drainage area) and proceeds in-stream to sediment/substrate descriptions. Such information will provide insight as to what organisms may be present or are expected to be



present, and to presence of stream impacts. The information requested in the Physical Characterization section of the Field Data Sheet is briefly discussed below:

Predominant Surrounding Land Use — Observe the prevalent land-use type in the vicinity (noting any other land uses in the area which, although not predominant, may potentially affect water quality).

Local Watershed Erosion — The existing or potential detachment of soil within the local watershed (the portion of the watershed that drains directly into the stream) and its movement into a stream are noted. Erosion can be rated through visual observation of watershed and stream characteristics. (Note any turbidity observed during water quality assessment below.)


Local Watershed Nonpoint Source Pollution — This item refers to problems and potential problems other than siltation. Nonpoint source pollution is defined as diffuse agricultural and urban runoff. Other compromising factors in a watershed that may affect water quality are feedlots, wetlands, septic systems, dams and impoundments, and/or mine seepage.

Estimated Stream Width (m) — Estimate the distance from shore to shore at a transect representative of the stream width in the area.

Estimated Stream Depth (m) — Riffle, run, and pool. Estimate the vertical distance from water surface to stream bottom at a representative depth at each of the three habitat types.

High Water Mark (m) — Estimate the vertical distance from the stream bank to the peak overflow level, as indicated by debris hanging in bank or floodplain vegetation, and deposition of silt or soil. In instances where bank overflow is rare, a high water mark may not be evident.

Velocity — Record an estimate of stream velocity in a representative run area. Dam Present — Indicate the presence or absence of a dam upstream or downstream of the sampling

station. If a dam is present, include specific information relating to alteration of flow. Channelized — Indicate whether or not the area around the sampling station is channelized. Canopy Cover — Note the general proportion of open to shaded area which best describes the amount

of cover at the sampling station. Sediment Odors — Disturb sediment and note any odors described (or include any other odors not

listed) which are associated with sediment in the area of the sampling station. Sediment Oils — Note the term which best describes the relative amount of sediment oils observed

in the sampling area. Sediment Deposits — Note those deposits described (or include any other deposits not listed) which

are present in the sampling area. Also indicate whether the undersides of rocks not deeply embedded are black (which generally indicates low dissolved oxygen or anaerobic conditions).

Inorganic Substrate Components — Visually estimate the relative proportion of each of the several substrate/particle types listed that are present in the sampling area.

Organic Substrate Components — Indicate relative abundance of each of the three substrate types listed.

Listed below is a general explanation of some major habitat parameters to be evaluated.

Substrate and In-Stream Cover

The in-stream habitat characteristics directly pertinent to the support of aquatic communities consist of substrate type and stability, availability of refugia, and migration/passage potential.

Bottom Substrate — This refers to the availability of habitat for support of aquatic organisms. A variety of substrate materials and habitat types is desirable. The presence of rock and gravel in flowing streams is generally considered the most desirable habitat. However, other forms of habitat may provide the niches required for community support. For example, logs, tree roots, submerged or emergent vegetation, undercut banks, etc., will provide excellent habitat for a variety of organisms, particularly fish. Bottom substrate is evaluated and rated by observation.

Embeddedness — The degree to which boulders, rubble, or gravel are surrounded by fine sediment indicates suitability of the stream substrate as habitat for benthic macroinvertebrates and for fish spawning and egg incubation. Embeddedness is evaluated by visual observation of the degree to which larger particles are surrounded by sediment. In some western areas of the United States, embeddedness is regarded as the stability of cobble substrate by measuring the depth of burial of large particles (cobble, boulders).

Stream Discharge and/or Stream Velocity — Stream discharge relates to the ability of a stream to provide and maintain a stable aquatic environment. Stream discharge (and water quality) is most critical to the support of aquatic communities when the representative low flow is ≤0.15 cms (5 cfs). In these small streams, discharge should be estimated in a straight stretch of run area where banks are parallel and bottom contour is relatively flat. Even where a few stations may have discharges in excess of 0.15 cms, discharge may still be the predominating constraint. Therefore, the evaluation is based on discharge rate rather than velocity.


In larger streams and rivers (>0.15 cms), velocity, in conjunction with depth, has a more direct influence than the discharge rate on the structure of benthic communities (Osborne and Hendricks 1983) and fish communities (Oswood and Barber 1982). The quality of the aquatic habitat can therefore be evaluated in terms of a velocity and depth relationship. As patterned after Oswood and Barber (1982), four general categories of velocity and depth are optimal for benthic and fish communities: (1) slow (<0.3 m/s), shallow (<0.5 m); (2) slow (<0.3 m/l), deep (>0.5 m); (3) fast (>0.3 m/s), deep (0.5 m); and (4) fast (>0.3 m/s), shallow (<0.5 m). Habitat quality is reduced in the absence of one or more of these four categories.

Channel Morphology

Channel morphology is determined by the flow regime of the stream, local geology, land surface form, soil, and human activities (Platts et al. 1983). The sediment movement along the channel, as influenced by the tractive forces of flowing water and the sinuosity of the channel, also affects habitat conditions.

Channel Alteration — The character of sediment deposits from upstream is an indication of the severity of watershed and bank erosion and stability of the stream system. The growth, or appearance, of sediment bars tends to increase with continued watershed disturbance. Channel alteration also results in deposition, which may occur on the inside of bends, below channel constrictions, and where stream gradient flattens out. Channelization (e.g., straightening, construction of concrete embankments) decreases stream sinuosity, thereby increasing stream velocity and the potential for scouring.

Bottom Scouring and Deposition — These parameters relate to the destruction of in-stream habitat resulting from the problems described above. Characteristics to observe are scoured substrate and degree of siltation in pools and riffles. Scouring results from high-velocity flows. The potential for scouring is increased by channelization. Deposition and scouring result from the transport of sediment or other particulates and may be an indication of large-scale watershed erosion. Deposition and scouring are rated by estimating the percentage of an evaluated reach that is scoured or silted (i.e., 50-ft silted in a 100-ft stream length equals 50%).

Pool/Riffle or Run/Bend Ratio — These parameters assume that a stream with riffles or bends provides more diverse habitat than a straight (run) or uniform depth stream. Bends are included because lowgradient streams may not have riffle areas, but excellent habitat can be provided by the cutting action of water at bends. The ratio is calculated by dividing the average distance between riffles or bends by the average stream width. If a stream contains riffles and bends, the dominant feature with the best habitat should be used.

Riparian and Bank Structure

Well-vegetated banks are usually stable regardless of bank undercutting; undercutting actually provides excellent cover for fish (Platts et al. 1983). The ability of vegetation and other materials on the stream banks to prevent or inhibit erosion is an important determinant of the stability of the stream channel and in-stream habitat for indigenous organisms. Because riparian and bank structure indirectly affect the in-stream habitat features, they are weighted less than the primary or secondary parameters.

The upper bank is the land area from the break in the general slope of the surrounding land to the normal high water line. The upper bank is normally vegetated and covered by water only during extreme high water conditions. Land forms vary from wide, flat floodplains to narrow, steep slopes. The lower bank is the intermittently submerged portion of the stream cross section from the normal high water line to the lower water line. The lower channel defines the stream width.

Bank Stability — Bank stability is rated by observing existing or potential detachment of soil from the upper and lower stream bank and its potential movement into the stream. Steeper banks are generally more subject to erosion and failure, and may not support stable vegetation. Streams with


poor banks will often have poor in-stream habitat. Adjustments should be made in areas with clay banks where steep, raw areas may not be as susceptible to erosion as other soil types.

Bank Vegetative Stability — Bank soil is generally held in place by plant root systems. Erosional protection may also be provided by boulder, cobble, or gravel material. An estimate of the density of bank vegetation (or proportion of boulder, cobble, or gravel material) covering the bank provides an indication of bank stability and potential in-stream sedimentation.

Streamside Cover — Streamside cover vegetation is evaluated in terms of stream-shading and escape cover or refuge for fish. A rating is obtained by visually determining the dominant vegetation type covering the exposed stream bottom, bank, and top of bank. Platts (1974) found that streamside cover consisting primarily of shrub had a higher fish standing crop than similar-size streams having tree or grass streamside cover. Riparian vegetation dominated by shrubs and trees provides the CPOM source in allochthonous systems.

Procedure for Performing the Habitat Assessment

1. Select the reach to be assessed. The habitat assessment is performed on the same 100-m reach (or other reach designation [e.g., 40 × stream wetted width]) from which the biological sampling is conducted. Some parameters require an observation of a broader section of the catchment than just the sampling reach.

2. Complete the station identification section of each field data sheet and habitat assessment form (Figures A.2 through A.7).

3. It is best for the investigators to obtain a close look at the habitat features to make an adequate assessment. If the physical and water quality characterization and habitat assessment are done before the biological sampling, care must be taken to avoid disturbing the sampling habitat.

4. Complete the Physical Characterization and Water Quality Field Data Sheet. Sketch a map of the sampling reach on the back of the form.

5. Complete the Habitat Assessment Field Data Sheet, in a team of two or more biologists, if possible, to come to a consensus on determination of quality. Those parameters to be evaluated on a scale greater than a sampling reach require traversing the stream corridor to the extent deemed necessary to assess the habitat feature. As a general rule-of-thumb, use two lengths of the sampling reach to assess these parameters.

Quality Assurance Procedures

1. Each biologist is to be trained in the visual-based habitat assessment technique for the applicable region or state.

2. The judgment criteria for each habitat parameter are calibrated for the stream classes under study. Some text modifications may be needed on a regional basis.

3. Periodic checks of assessment results are completed using pictures of the sampling reach and discussions among the biologists in the agency.

REFERENCES

Ball, J. Stream Classification Guidelines for Wisconsin. Wisconsin Department of Natural Resources Technical Bulletin, Wisconsin Department of Natural Resources, Madison, WI. 1982.

Barbour, M.T. and J.B. Stribling. Use of habitat assessment in evaluating the biological integrity of stream communities, in Biological Criteria: Research and Regulation. Edited by G. Gibson. Proceedings of a Symposium, Office of Water, U.S. Environmental Protection Agency, Washington, D.C. EPA-440-5-91005. 1991.

Barbour, M.T. and J.B. Stribling. A technique for assessing stream habitat structure, in Conference Proceedings, Riparian Ecosystems in the Humid U.S.: Functions, Values and Management. National Assoc. of Conservation Districts, Washington, D.C., Atlanta, GA., pp. 156–178. 1994.

EPA. Methods for Measuring the Toxicity and Bioaccumulation of Sediment-Associated Contaminants with Freshwater Invertebrates. 2nd edition. EPA series number pending, Duluth, MN. 1999.


EPA. Rapid Bioassessment Protocols for Use in Wadeable Streams and Rivers: Periphyton, Benthic Macroinvertebrates and Fish. Office of Water, U.S. Environmental Protection Agency, Washington, D.C. EPA 841/B-99/002. 1999.

Hannaford, M.J., M.T. Barbour, and V.H. Resh. Training reduces observer variability in visual-based assessments of stream habitat. J. North Am. Benthol. Soc., 16: 853–860. 1997.

Hawkins, C.P., J.L. Kersher, P.A. Bisson, M.D. Bryant, L.M. Decker, S.V. Gregory, D.A. McCullough, C.K. Overton, G.H. Reeves, R.J. Steedman, and M.K. Young. A hierarchical approach to classifying stream habitat features. Fisheries, 18: 3–12. 1993.

Kaufmann, P.R. and E.G. Robison. Physical habitat assessment, in Environmental Monitoring and Assessment Program. Edited by D.J. Klemm and J.M. Lazorchak. 1994 Pilot Field Operations Manual for Stream. Environmental Monitoring Systems Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH. EPA/620/R-94/004. pp. 6-1 to 6-38. 1994.

Klemm, D.J. and J.M. Lazorchak. Environmental Monitoring and Assessment Program. 1994. Pilot Field Operations Manual for Stream. Environmental Monitoring Systems Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH. EPA/620/R-94/004. 1994.

Leopold, L.B., M.G. Wolman, and J.P. Miller. Fluvial Processes in Geomorphology. W.H. Freeman, San Francisco, CA. 1964.

MACS (Mid-Atlantic Coastal Streams Workgroup). Standard Operating Procedures and Technical Basis: Macroinvertebrate Collection and Habitat Assessment for Low-Gradient Nontidal Streams. Delaware Dept. Natural Resources and Environ. Conservation, Dover, DE. 1996.

Meador, M.R., C.R. Hupp, T.F. Cuffney, and M.E. Gurtz. Methods for Characterizing Stream Habitat as Part of the National Water-Quality Assessment Program. U.S. Geological Survey Open-File Report, Raleigh, NC. USGS/OFR 93-408. 1993.

OEPA (Ohio Environmental Protection Agency). Biological Criteria for the Protection of Aquatic Life: Volume II. User’s Manual for Biological Assessment of Ohio Surface Waters. Ohio Environmental Protection Agency, Columbus, OH. 1987.

OEPA (Ohio Environmental Protection Agency). The Qualitative Habitat Evaluation Index (QHEI): Rationale, Methods, and Application. Ecological Assessment Section, Ohio Environmental Protection Agency, Columbus, OH. 1989.

Osborne, L.L. and E.E. Hendricks. Streamflow and Velocity as Determinants of Aquatic Insect Distribution and Benthic Community Structure in Illinois. Water Resources Center, University of Illinois, Report No. UILU-WRC-83-183, U.S. Department of the Interior, Bureau of Reclamation. 1983.

Oswood, M.E. and W.E. Barber. Assessment of fish habitat in streams: goals, constraints, and a new technique. Fisheries, 7: 8–11 (1982).

Plafkin, J.L., M.T. Barbour, K.D. Porter, S.K. Gross, and R.M. Hughes. Rapid Bioassessment Protocols for Use in Streams and Rivers: Benthic Macroinvertebrates and Fish. EPA-440-4-89-001. U.S. Environmental Protection Agency. Office of Water Regulations and Standards. Washington, D.C. 1989.

Platts, W.S. Geomorphic and Aquatic Conditions Influencing Salmonids and Stream Classification with Application to Ecosystem Management. U.S. Department of Agriculture SEAM program, Billings, MT. 1974.

Platts, W.S., W.F. Megahan, and G.W. Minshall. Methods for Evaluating Stream, Riparian and Biotic Conditions. U.S. Department of Agriculture General Technical Report INT-138, Ogden, UT. 1983.

Rankin, E.T. The use of the qualitative habitat evaluation index for use attainability studies in streams and rivers in Ohio, in Biological Criteria: Research and Regulation. Edited by G. Gibson. Office of Water, U.S. Environmental Protection Agency, Washington, D.C. EPA 440/5-91-005. 1991.

Rankin, E.T. Habitat indices in water resource quality assessments, in Biological Assessment and Criteria: Tools for Water Resource Planning and Decision Making. Edited by W.S. Davis, and T.P. Simon. Lewis Publ., Boca Raton, FL., pp. 181–208. 1995.

Rosgen, D. A stream classification system, in Riparian Ecosystems and their Management. First North American Riparian Conference. Rocky Mountain Forest and Range Experiment Station, RM-120. pp. 91–95. 1985.

Rosgen, D. A classification of natural rivers. Catena, 22: 169–199. 1994. Rosgen, D. Applied River Morphology. Wildland Hydrology Books, Pagosa Spring, CO. 1996.

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