BUREAU OF CLEAN WATER. Appendix C Biological Field Methods C1. Habitat Assessment DECEMBER 2013

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1 BUREAU OF CLEAN WATER Appendix C Biological Field Methods C1. Assessment DECEMBER 2013

2 HABITAT ASSESSMENT The Department has adopted the habitat assessment methods outlined in EPA s Rapid Bioassessment Protocols (Plafkin, et al. 1989) and subsequently modified 1. The matrix used to assess habitat quality is based on key physical characteristics of the waterbody and surrounding lands. All parameters evaluated represent potential limitations to the quality and quantity of instream habitat available to aquatic biota. These, in turn, affect community structure and composition. The main purpose of the habitat assessment is to account for the limitations that are due to existing stream conditions. This is particularly important in cause/effect and cumulative impact studies where the benthic community at any given station may already be self-limited by background watershed and habitat conditions or impacts from current land uses. In order to minimize the effects of habitat variability, every effort is made to sample similar habitats at all stations. The habitat assessment process involves rating twelve 1 parameters as excellent, good, fair, or poor, by assigning a numeric value (ranging from ), based on the criteria included on the Assessment Field Data Sheets (Riffle/Run, Glide/Pool and Multihabitat, Appendix A). The twelve habitat assessment parameters used in the PaDEP-RBP evaluations for Riffle/Run prevalent (and Glide/Pool prevalent) streams are discussed below. The Glide/Pool parameters that differ from the Riffle/Run parameters are shown in italics. The first four parameters evaluate stream conditions in the immediate vicinity of the benthic macroinvertebrate sampling point: Instream Fish Cover - evaluates the percent makeup of the substrate (boulders, cobble, other rock material) and submerged objects (logs, undercut banks) that provide refuge for fish. Epifaunal Substrate - evaluates riffle quality, i.e. areal extent relative to stream width and dominant substrate materials that are present. (In the absence of well-defined riffles, this parameter evaluates whatever substrate is available for aquatic invertebrate colonization.) Embeddedness - estimates the percent (vertical depth) of the substrate interstitial spaces filled with fine sediments. (pool substrate characterization: evaluates the dominant type of substrate materials, i.e. gravel, mud, root mats, etc. that are more commonly found in glide/pool habitats.) Velocity/Depth Regime - evaluates the presence/absence of four velocity/depth regimes - fast-deep, fast-shallow, slow-deep, and slow-shallow. (Generally, shallow is <0.5m and slow is <0.3m/sec. Pool variability: describes the presence and dominance of several pool depth regimes.) The next four parameters evaluate a larger area surrounding the sampled riffle. As a rule of thumb, this expanded area is the stream length defined by how far upstream and downstream the investigator can see from the sample point. 1. Plafkin et al. originally presented nine habitat assessment parameters divided into three different scoring ranges of 20-0, 15-0, and Modifications to these original habitat methods were presented at several seminars following this 1989 publication. These modifications added one more habitat parameter to each of the three original categories; bringing the total parameters to 12. The scoring ranges eventually were increased to 20-0 for all 12. This Protocol has undergone several more iterations resulting in yet more variations from the original and the Department s current 12 criteria - 20 point scoring habitat assessment method. 1

3 Channel Alteration - primarily evaluates the extent of channelization or dredging but can include any other forms of channel disruptions that would be detrimental to the habitat. Sediment Deposition - estimates the extent of sediment effects in the formation of islands, point bars, and pool deposition. Riffle Frequency (pool/riffle or run/bend ratio) - estimates the frequency of riffle occurrence based on stream width. (channel sinuosity: the degree of sinuosity to total length of the study segment.) Channel Flow Status - estimates the areal extent of exposed substrates due to water level or flow conditions. The next four parameters evaluate an even greater area. This area is usually defined as the length of stream that was electroshocked for fish (or an approximate 100 meter stream reach when no fish were sampled). It can also take into consideration upstream land-use activities in the watershed: Condition of Banks - evaluates the extent of bank failure or signs of erosion. Bank Vegetative Protection - estimates the extent of stream bank that is covered by plant growth providing stability through well-developed root systems. Grazing or Other Disruptive Pressures - evaluates disruptions to surrounding land vegetation due to common human activities, such as crop harvesting, lawn care, excavations, fill, construction projects, and other intrusive activities. Riparian Vegetative Zone Width - estimates the width of protective buffer strips or riparian zones. This is a rating of the buffer strip with the least width. It is best to conduct the habitat assessment after sampling since the investigator has observed all conditions in the sampled segment and immediate surrounding watershed. After all parameters in the matrix are evaluated and scored, the scores are summed to derive a habitat score for that station. The optimal category scores range from ; suboptimal from ; marginal from ; and poor is 60 or less. The gaps between these categories are left to the discretion of the investigator s best professional judgment. REFERENCES 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/ U.S. Environmental Protection Agency, Office of Water, Washington, D.C. 2

4 APPENDIX A HABITAT ASSESSMENT DATA SHEETS RIFFLE/RUN & GLIDE/POOL & MULTIHABITAT 3

5 3800-FM-BPNPSM0402 4/2012 COMMONWEALTH OF PENNSYLVANIA DEPARTMENT OF ENVIRONMENTAL PROTECTION BUREAU OF POINT AND NON-POINT SOURCE MANAGEMENT WATER QUALITY NETWORK HABITAT ASSESSMENT WATERBODY NAME STR CODE/RMI STATION NUMBER DATE AQUATIC ECOREGION LOCATION TIME COUNTY INVESTIGATORS FORM COMPLETED BY 1. Instream Cover (Fish) RIFFLE/RUN PREVALENCE Category Greater than 50% mix of boulder, cobble, submerged logs, undercut banks, or other stable habitat % mix of boulder, cobble, or other stable habitat; adequate habitat % mix of boulder, cobble, or other stable habitat; habitat availability less than desirable. Less than 10% mix of boulder, cobble, or other stable habitat; lack of habitat is obvious. 2. Epifaunal Substrate Well developed riffle and run, riffle is as wide as stream and length extends two times the width of stream; abundance of cobble. Riffle is as wide as stream but length is less than two times width; abundance of cobble; boulders and gravel common. Run area may be lacking; riffle not as wide as stream and its length is less than two times the stream width; gravel or large boulders and bedrock prevalent; some cobble present. Riffles or run virtually nonexistent; large boulders and bedrock prevalent; cobble lacking. 3. Embeddedness Gravel, cobble, and boulder particles are 0-25% surrounded by fine sediment. Gravel, cobble, and boulder particles are 25-50% surrounded by fine sediment. Gravel, cobble, and boulder particles are 50-75% surrounded by fine sediment. Gravel, cobble, and boulder particles are more than 75% surrounded by fine sediment. 4. Velocity/Depth Regimes All four velocity/depth regimes present (slowdeep, slow-shallow, fastdeep, fast-shallow). Only 3 of the 4 regimes present (if fast-shallow is missing, score lower than if missing other regimes). Only 2 of the 4 habitat regimes present (if fastshallow or slow-shallow are missing, score lower than if missing other regimes). Dominated by 1 velocity/depth regime (usually slowdeep). 5. Channel Alteration No channelization or dredging present. Some channelization present, usually in areas of bridge abutments; evidence of past channelization, i.e., dredging, (greater than past 20 yr) may be present, but recent channelization is not present. New embankments present on both banks; and 40-80% of stream reach channelized and disrupted. Banks shored gabion or cement; over 80% of the stream reach channelized and disrupted. Total Side 1 4

6 3800-FM-BPNPSM0402 4/2012 RIFFLE/RUN PREVALENCE Category 6. Sediment Deposition Little or no enlargement of islands or point bars and less than 5% of the bottom affected by sediment deposition. Some new increase in bar formation, mostly from coarse gravel; 5-30% of the bottom affected; slight deposition in pools. Moderate deposition of new gravel, coarse sand on old and new bars; 30-50% of the bottom affected; sediment deposits at obstruction, constriction, and bends; moderate deposition of pools prevalent. Heavy deposits of fine material, increased bar development; more than 50% of the bottom changing frequently; pools almost absent due to substantial sediment deposition. 7. Frequency of Riffles Occurrence of riffles relatively frequent; distance between riffles divided by the width of the stream equals 5 to 7; variety of habitat. Occurrence of riffles infrequent; distance between riffles divided by the width of the stream equals 7 to 15. Occasional riffle or bend; bottom contours provide some habitat; distance between riffles divided by the width of the stream is between 15 to 25. Generally all flat water or shallow riffles; poor habitat; distance between riffles divided by the width of the stream is between ratio > Channel Flow Status Water reaches base of both lower banks and minimal amount of channel substrate is exposed. Water fills > 75% of the available channel; or <25% of channel substrate is exposed. Water fills 25-75% of the available channel and/or riffle substrates are mostly exposed. Very little water in channel and mostly present as standing pools. 9. Condition of Banks Banks stable; no evidence of erosion or bank failure. Moderately stable; infrequent, small areas of erosion mostly healed over. Moderately unstable; up to 60% of banks in reach have areas of erosion. Unstable; many eroded areas; raw areas frequent along straight sections and bends; on side slopes, % of bank has erosional scars. 10. Bank Vegetative Protection More than 90% of the streambank surface covered by vegetation % of the streambank surface covered by vegetation % of the streambank surfaces covered by vegetation. Less than 50% of the streambank surface covered by vegetation. 11. Grazing or Other Disruptive Pressure Vegetative disruption, through grazing or mowing, minimal or not evident; almost all plants allowed to grow naturally. Disruption evident but not affecting full plant growth potential to any great extent; more than one-half of the potential plant stubble height remaining. Disruption obvious; patches of bare soil or closely cropped vegetation common; less than one-half of the potential plant stubble height remaining. Disruption of vegetation is very high; vegetation has been removed to 2 inches or less in average stubble height. 12. Riparian Vegetative Zone Width >18 meters; human activities (i.e., parking lots, roadbeds, clearcuts, lawns, or crops) have not impacted zone meters; human activities have impacted zone only minimally meters; human activities have impacted zone a great deal. <6 meters; little or no riparian vegetation due to human activities. Total Side 2 Total Score 5

7 3800-FM-WSFR0079 9/2005 COMMONWEALTH OF PENNSYLVANIA DEPARTMENT OF ENVIRONMENTAL PROTECTION BUREAU OF WATER STANDARDS AND FACILITY REGULATION HABITAT ASSESSMENT FIELD DATA SHEET DATE TIME INITIALS: 1. Instream Cover (Fish) GLIDE/POOL PREVALENCE Category Greater than 50% mix of snags, submerged logs, undercut banks, or other stable habitat; rubble, gravel may be present % mix of boulder, cobble, or other stable habitat; adequate habitat % mix of boulder, cobble, or other stable habitat; habitat availability less than desirable. Less than 10% mix of boulder, cobble, or other stable habitat; lack of habitat is obvious. 2. Epifaunal Substrate Preferred benthic substrate (to be sampled) abundant throughout stream site and at stage to allow full colonization potential (i.e., logs, snags that are not new fall and not transient). Substrate common but not prevalent or well suited for full colonization potential. Substrate frequently disturbed or removed. Substrate unstable or lacking. 3. Pool Substrate Characterization Mixture of substrate materials, with gravel and firm sand prevalent; root mats and submerged vegetation common. Mixture of soft sand, mud, or clay; mud may be dominant; some root mats and submerged vegetation present. All mud or clay or sand bottom; little or no root mat; no submerged vegetation. Hard-pan clay or bedrock; no root mat or vegetation. 4. Pool Variability Even mix of largeshallow, large-deep, small-shallow, smalldeep pools present. Majority of pools largedeep; very few shallow. Shallow pools much more prevalent than deep pools. Majority of pools smallshallow or pools absent. 5. Channel Alteration No channelization or dredging present. Some channelization present, usually in areas of bridge abutments; evidence of past channelization, i.e., dredging, (greater than past 20 yr.) may be present, but recent channelization is not present. New embankments present on both banks; channelization may be extensive, usually in urban areas or drainage areas of agriculture lands; and >80% of stream reach channelized and disrupted. Extensive channelization; banks shored with gabion or cement; heavily urbanized areas; instream habitat greatly altered or removed entirely. 6. Sediment Deposition Less than 20% of bottom affected; minor accumulation of fine and coarse material at snags and submerged vegetation; little or no enlargement of islands or point bars % affected; moderate accumulation; substantial sediment movement only during major storm event; some new increase in bar formation % affected; major deposition; pools shallow, heavily silted; embankments may be present on both banks; frequent and substantial sediment movement during storm events. Channelized; mud, silt, and/or sand in braided or non-braided channels; pools almost absent due to substantial sediment deposition. TOTAL (Side 1): 6

8 3800-FM-WSFR0079 9/2005 GLIDE/POOL PREVALENCE 7. Channel Sinuosity The bends in the stream increase the stream length 3 to 4 times longer than if it was in a straight line. Category The bends in the stream increase the stream length 2 to 3 times longer than if it was in a straight line. The bends in the stream increase the stream length 1 to 2 times longer than if it was in a straight line. Channel straight; waterway has been channelized for a long distance. 8. Channel Flow Status Water reaches base of both lower banks and minimal amount of channel substrate is exposed. Water fills >75% of the available channel; or <25% of channel substrate is exposed. Water fills 25-75% of the available channel and/or riffle substrates are mostly exposed. Very little water in channel and mostly present as standing pools. 9. Condition of Banks Banks stable; no evidence of erosion or bank failure; side slopes generally <30%; little potential for future problems. Moderately stable; infrequent, small areas of erosion mostly healed over; side slopes up to 40% on one bank; slight erosion potential in extreme floods. Moderately unstable; moderate frequency and size of erosional areas; side slopes up to 60% on some banks; high erosion potential during extremely high flow. Unstable; many eroded areas; raw areas frequent along straight sections and bends; side slopes >60% common. 10. Bank Vegetative Protection More than 90% of the streambank surface covered by vegetation % of the streambank surfaces covered by vegetation % of the streambank surfaces covered by vegetation. Less than 50% of the streambank surfaces covered by vegetation. 11. Grazing or Other Disruptive Pressure Vegetative disruption is minimal or not evident; almost all plants allowed to grow naturally. Disruption evident but not affecting full plant growth potential to any great extent; more than one-half of the potential plant stubble height remaining. Disruption obvious; patches of bare soil or closely cropped vegetation common; less than one-half of the potential plant stubble height remaining. Disruption of streambank vegetation is very high; vegetation has been removed to 2 inches or less in average stubble height. 12. Riparian Vegetative Zone Width (least buffered side) >18 meters; human activities (i.e., parking lots, roadbeds, clearcuts, lawns, or crops) have not impacted zone meters; human activities have impacted zone only minimally meters; human activities have impacted zone a great deal. <6 meters; little or no riparian vegetation due to human activities. TOTAL (Side 2): (Side 1): STATION : 7

9 s to be evaluated in sampling reach 3800-FM-WSFR /2007 COMMONWEALTH OF PENNSYLVANIA DEPARTMENT OF ENVIRONMENTAL PROTECTION BUREAU OF WATER STANDARDS AND FACILITY REGULATION HABITAT ASSESSMENT FIELD DATA SHEET LOW GRADIENT STREAMS (FRONT) STREAM NAME LOCATION STATION # RIVERMILE STREAM CLASS LAT LONG RIVER BASIN STORET # AGENCY INVESTIGATIONS FORM COMPLETED BY DATE TIME REASON FOR SURVEY AM PM 1. Epifaunal Substrate/Available Cover 2. Pool Substrate Characterization 3. Pool Variability 4. Sediment Deposition 5. Channel Flow Status Condition Category Greater than 50% of subsrate favorable for epifaunal colonization and fish cover; mix of snags, submerged logs, undercut banks, cobble or other stable habitat at stage to allow full colonization potential (i.e., logs/snags that are not new fall and not transient) % mix of stable habitat; well-suited for full colonization potential; adequate habitat for maintenance of populations; presence of additional substrate in the form of newfall, but not yet prepared for colonization (may rate at high end of scale) 10-30% mix of stable habitat; habitat availability less than desirable; substrate frequently disturbed or removed. Less than 10% stable habitat; lack of habitat is obvious; substrate unstable or lacking Mixture of substrate materials, with gravel and firm sand prevalent; root mats and submerged vegetation common. Mixture of soft sand, mud, or clay; mud may be dominant; some root mats and submerged vegetation present. All mud or clay or sand bottom; little or no root mat; no submerged vegetation. Hard-pan clay or bedrock; no root mat or vegetation Even mix of largeshallow, large-deep, small-shallow, smalldeep pools present. Majority of pools largedeep; very few shallow. Shallow pools much more prevalent than deep pools. Majority of pools smallshallow or pools absent Little or no enlargement of islands or point bars and less then <20% of the bottom affected by sediment deposition. Some new increase in bar formation, mostly from gravel, sand or fine sediment; 20-50% of the bottom affected; slight deposition in pools. Moderate deposition of new gravel, sand or fine sediment on old and new bars; 50-80% of the bottom affected; sediment deposits at obstructions, constrictions, and bends; moderate deposition of pools prevalent. Heavy deposits of fine material, increased bar development; more than 80% of the bottom changing frequently; pools almost absent due to substantial sediment deposition Water reaches base of both lower banks, and minimal amount of channel substrate is exposed. Water fills >75% of the available channel; or <25% of channel substrate is exposed. Water fills 25-75% of the available channel, and/or riffle substrates are mostly exposed. Very little water in channel and mostly present as standing pools

10 s to be evaluated in sampling reach 3800-FM-WSFR /2007 HABITAT ASSESSMENT FIELD DATA SHEET LOW GRADIENT STREAMS (BACK) Condition Category 6. Channel Alteration Channelization or dredging absent or minimal; stream with normal pattern. Some channelization present, usually in areas of bridge abutments; evidence of past channelization, i.e., dredging, (greater than past 20 yr) may be present, but recent channelization is not present. Channelization may be extensive; embankments or shoring structures present on both banks; and 40 to 80% of stream reach channelized and disrupted. Banks shored with gabion or cement; over 80% of the stream reach channelized and disrupted. Instream habitat greatly altered or removed entirely Bank Stability (score each bank) Banks stable; evidence of erosion or bank failure absent or minimal; little potential for future problems. <5% of bank affected. Moderately stable; infrequent, small areas of erosion mostly sealed over. 5-30% of bank in reach has areas of erosion. Moderately unstable; 30-60% of bank in reach has areas of erosion; high erosion potential during floods Unstable; many eroded areas; raw areas frequent along straight sections and bends; obvious bank sloughing; % of bank has erosional scars. (LB) (RB) 8. Vegetative Protection (score each bank) Note: determine left or right side by facing downstream. (LB) (RB) Left Bank Right Bank More than 90% of the streambank surfaces and immediate riparian zone covered by native vegetation, including trees, understory shrubs, or nonwoody macrophytes; vegetative disruption through grazing or mowing minimal or not evident; almost all plants allowed to grow naturally % of the streambank surfaces covered by native vegetation, but one class of plants is not well-represented; disruption evident but not affecting full plant growth potential to any great extent; more than one-half of the potential plant stubble height remaining % of the streambank surfaces covered by vegetation; disruption obvious; patches of bare soil or closely cropped vegetation common; less than one-half of the potential plant stubble height remaining. Less than 50% of the streambank surfaces covered by vegetation; disruption of streambank vegetation is very high; vegetation has been removed to 5 centimeters or less in stubble height. Left Bank Right Bank Riparian Vegetative Zone Width (score each bank riparian zone) >18 meters; human activities (i.e., parking lots, roadbeds, clearcuts, lawns, or crops) have not impacted zone meters; human activities have impacted zone only minimally meters; human activities have impacted zone only minimally. <6 meters; little or not riparian vegetation due to human activities. (LB) (RB) Left Bank Right Bank Total Score 9