Combination of Biological and Habitat Indices for Assessment of Idaho Streams

States and tribes are encouraged to use multiple biological assemblages in assessment of water bodies. An assessment index for each assemblage provides information on aspects of the aquatic resource that may be unique in terms of stressor sensitivity, stressor type, or ecological scale. However, assessment results relative to impairment thresholds can disagree among indices for an individual water body, leading to uncertain overall water‐body assessments. We explored options for combining stream indices for macroinvertebrates, fish, and habitat in ways that would yield the most consistent and sensitive results relative to established disturbance categories. Methods varied in the scoring or rating scales used to standardize each index value, the thresholds used to define impairment of aquatic life uses, and the ways of synthesizing multiple indices. The index compositing method that scores each index on a continuous scale and averages the scores after standardizing had superior accuracy, sensitivity, and precision. In addition, using the 25th quantile of reference sites instead of the 10th quantile resulted in a more balanced error rate among reference and degraded site categories.     

A Biological Assessment of Streams in the Eastern United States Using a Predictive Model for Macroinvertebrate Assemblages1

Abstract: A predictive model (RIVPACS‐type) for benthic macroinvertebrates was constructed to assess the biological condition of 1,087 streams sampled throughout the eastern United States from 1993‐2003 as part of the U.S. Geological Survey’s National Water‐Quality Assessment Program. A subset of 338 sites was designated as reference quality, 28 of which were withheld from model calibration and used to independently evaluate model precision and accuracy. The ratio of observed (O) to expected (E) taxa richness was used as a continuous measure of biological condition, and sites with O/E values <0.8 were classified as biologically degraded. Spatiotemporal variability of O/E values was evaluated with repeated annual and within‐site samples at reference sites. Values of O/E were regressed on a measure of urbanization in three regions and compared among streams in different land‐use settings. The model accurately predicted the expected taxa at validation sites with high precision (SD = 0.11). Within‐site spatial variability in O/E values was much larger than annual and among‐site variation at reference sites and was likely caused by environmental differences among sampled reaches. Values of O/E were significantly correlated with basin road density in the Boston, Massachusetts (p < 0.001), Birmingham, Alabama (p = 0.002), and Green Bay, Wisconsin (p = 0.034) metropolitan areas, but the strength of the relations varied among regions. Urban streams were more depleted of taxa than streams in other land‐use settings, but larger networks of riparian forest appeared to mediate biological degradation. Taxa that occurred less frequently than predicted by the model were those known to be generally intolerant of a variety of anthropogenic stressors.     

An Evaluation of Qualitative Indexes of Physical Habitat Applied to Agricultural Streams in Ten U.S. States1

Hughes, Robert M., Alan T. Herlihy, and Philip R. Kaufmann, 2010. An Evaluation of Qualitative Indexes of Physical Habitat Applied to Agricultural Streams in Ten U.S. States. Journal of the American Water Resources Association (JAWRA) 46(4): 792-806. DOI: 10.1111/j.1752-1688.2010.00455.x Abstract: Assessment of stream physical habitat condition is important for evaluating stream quality globally. However, the diversity of metrics and methods for assessing physical habitat condition confounds comparisons among practitioners. We surveyed 51 previously sampled stream sites (0.0-6.3 m wide) located in regions of row-crop agriculture in Oregon, California, North Dakota, South Dakota, Nebraska, Iowa, Minnesota, Pennsylvania, Maryland, and West Virginia to evaluate the comparability of four indexes of physical habitat condition relative to each other. We also compared the indexes to previously calculated indexes of fish and macroinvertebrate condition. The physical habitat indexes included the Stream Visual Assessment Protocol Version 2 of the Natural Resources Conservation Service, the qualitative habitat evaluation index of the Ohio Environmental Protection Agency, the rapid bioassessment protocol of the United States Environmental Protection Agency (USEPA), and a qualitative physical habitat index based on USEPA quantitative physical habitat measurements. All four indexes were highly correlated with each other, but low-to-moderately correlated with biotic index scores for fish and macroinvertebrate assemblages. Moderately high correlations occurred between some macroinvertebrate biotic index scores and quantitative metrics. We conclude that additional research is needed to increase the predictive and diagnostic capabilities of qualitative physical habitat indexes.     

Reach‐Scale Comparison of Habitat and Mollusk Assemblages for Select Sites in the Clinch River with Regional Context

Several hypotheses, including habitat degradation and variation in fluvial geomorphology, have been posed to explain extreme spatial and temporal variation in Clinch River mollusk assemblages. We examined associations between mollusk assemblage metrics (richness, abundance, recruitment) and physical habitat (geomorphology, streambed composition, fish habitat, and riparian condition) at 10 sites selected to represent the range of current assemblage condition in the Clinch River. We compared similar geomorphological units among reaches, employing semi‐quantitative and quantitative protocols to characterize mollusk assemblages and a mix of visual assessments and empirical measurements to characterize physical habitat. We found little to no evidence that current assemblage condition was associated with 54 analyzed habitat metrics. When compared to other sites in the Upper Tennessee River Basin (UTRB) that once supported or currently support mollusk assemblages, Clinch River sites were more similar to each other, representing a narrower range of conditions than observed across the larger geographic extent of the UTRB. A post‐hoc analysis suggested stream size and average boundary shear stress at bankfull stage may have historically limited species richness in the UTRB (p < 0.001). Associations between mollusk assemblages and physical habitat in the UTRB and Clinch River currently appear obscured by other factors limiting richness, abundance, and recruitment.     

Effects of Bioengineered Streambank Stabilization on Bank Habitat and Macroinvertebrates in Urban Streams

Non-structural streambank stabilization, or bioengineering, is a common stream restoration practice used to slow streambank erosion, but its ecological effects have rarely been assessed. We surveyed bank habitat and sampled bank macroinvertebrates at four bioengineered sites, an unrestored site, and a comparatively less-impacted reference site in the urban Peachtree-Nancy Creek catchment in Atlanta, GA, USA. The amount of organic bank habitat (wood and roots) was much higher at the reference site and three of the bioengineered sites than at the unrestored site or the other bioengineered site, where a very different bioengineering technique was used (“joint planting”). At all sites, we saw a high abundance of pollution-tolerant taxa, especially chironomids and oligochaetes, and a low richness and diversity of the bank macroinvertebrate community. Total biomass, insect biomass, and non-chironomid insect biomass were highest at the reference site and two of the bioengineered sites (p < 0.05). Higher biomass and abundance were found on organic habitats (wood and roots) versus inorganic habitats (mud, sand, and rock) across all sites. Percent organic bank habitat at each site proved to be strongly positively correlated with many factors, including taxon richness, total biomass, and shredder biomass. These results suggest that bioengineered bank stabilization can have positive effects on bank habitat and macroinvertebrate communities in urban streams, but it cannot completely mitigate the impacts of urbanization.     

A Comparison of Protocols and Observer Precision for Measuring Physical Stream Attributes1

Abstract: Stream monitoring programs commonly measure physical attributes to assess the effect of land management on stream habitat. Variability associated with the measurement of these attributes has been linked to a number of factors, but few studies have evaluated variability due to differences in protocols. We compared six protocols, five used by the U.S. Department of Agriculture Forest Service and one by the U.S. Environmental Protection Agency, on six streams in Oregon and Idaho to determine whether differences in protocol affect values for 10 physical stream attributes. Results from Oregon and Idaho were combined for groups participating in both states, with significant differences in attribute means for 9 out of the 10 stream attributes. Significant differences occurred in 5 of 10 in Idaho, and 10 of 10 in Oregon. Coefficients of variation, signal‐to‐noise ratio, and root mean square error were used to evaluate measurement precision. There were differences among protocols for all attributes when states were analyzed separately and as a combined dataset. Measurement differences were influenced by choice of instruments, measurement method, measurement location, attribute definitions, and training approach. Comparison of data gathered by observers using different protocols will be difficult unless a core set of protocols for commonly measured stream attributes can be standardized among monitoring programs.     

Relative Influence of Streamflows in Assessing Temporal Variability in Stream Habitat1

Abstract: The effects of streamflows on temporal variation in stream habitat were analyzed from the data collected 6‐11 years apart at 38 sites across the United States. Multiple linear regression was used to assess the variation in habitat caused by streamflow at the time of sampling and high flows between sampling. In addition to flow variables, the model also contained geomorphic and land use factors. The regression model was statistically significant (p < 0.05; R² = 0.31‐0.46) for 5 of 14 habitat variables: mean wetted stream depth, mean bankfull depth, mean wetted stream width, coefficient of variation of wetted stream width, and the percent frequency of bank erosion. High flows between samples accounted for about 16% of the total variation in the frequency of bank erosion. Streamflow at the time of sampling was the main source of variation in mean stream depth and contributed to the variation in mean stream width and the frequency of bank erosion. Urban land use (population change) accounted for over 20% of the total variation in mean bankfull depth, 15% of the total variation in the coefficient of variation of stream width, and about 10% of the variation in mean stream width.     

A Sampler for Measuring Deposited Fine Sediments in Streams1

Turner, Andy W., Jeff J. Hillis, and Charles F. Rabeni, 2012. A Sampler for Measuring Deposited Fine Sediments in Streams. Journal of the American Water Resources Association (JAWRA) 48(2): 366‐378. DOI: 10.1111/j.1752‐1688.2011.00618.x Abstract: Improvements and standardization of methodologies to quickly and accurately quantify deposited sediment in streams will allow advances in our understanding of biological effects of sedimentation. Most methods used to evaluate streambed conditions as part of biological monitoring or assessment programs are selected for ease of use, but can be subjective, inappropriate, and often of unknown accuracy. We developed a portable, light‐weight device to quantify deposited unconsolidated sediment (particles <2 mm) in wadeable streams. This deposited sediment sampler is a hand‐held unit that circumscribes an area of the streambed and through suction creates a force that suspends unconsolidated materials into a collector. Laboratory evaluations determined the efficiency (percent of available deposited sediment recovered) of the sampler to collect different sizes and concentrations of deposited sediment under differing streambed conditions, which allowed appropriate correction factors to be applied to each of four categories of streambed particle size. Field trials comparing our sampler to other methods commonly used by many state and federal agencies showed high comparability. The sampler can be constructed in just a few hours from inexpensive, easily obtained materials.     

Designing Impact Assessments for Evaluating Ecological Effects of Agricultural Conservation Practices on Streams1

Abstract: Conservation practices are regularly implemented within agricultural watersheds throughout the United States without evaluating their ecological impacts. Impact assessments documenting how habitat and aquatic biota within streams respond to these practices are needed for evaluating the effects of conservation practices. Numerous sampling protocols have been developed for monitoring streams. However, protocols designed for monitoring studies are not appropriate for impact assessments. We developed guiding principles for designing impact assessments of ecological responses to conservation practices. The guiding principles are as follows: (1) develop the hypothesis first, (2) use replicated experimental designs having controls and treatments, (3) assess the habitat and biological characteristics with quantitative and repeatable sampling methods, (4) use multiple sampling techniques for collecting aquatic organisms, and (5) standardize sampling efforts for aquatic organisms. The guiding principles were applied in designing a study intended to evaluate the influence of herbaceous riparian buffers on channelized headwater streams in central Ohio. Our example highlights that the application of our recommendations will result in impact assessments that are hypothesis‐driven and incorporate quantitative methods for the measurement of abiotic and biotic attributes.     

A Regional‐Scale Habitat Suitability Model to Assess the Effects of Flow Reduction on Fish Assemblages in Michigan Streams1

Zorn, Troy G., Paul W. Seelbach, and Edward S. Rutherford, 2012. A Regional‐Scale Habitat Suitability Model to Assess the Effects of Flow Reduction on Fish Assemblages in Michigan Streams. Journal of the American Water Resources Association (JAWRA) 48(5): 871‐895. DOI: 10.1111/j.1752‐1688.2012.00656.x Abstract: In response to concerns over increased use and potential diversion of Michigan’s freshwater resources, and the resulting state legislative mandate, an advisory council created an integrated assessment model to determine the potential for water withdrawals to cause an adverse resource impact to fish assemblages in Michigan’s streams. As part of this effort, we developed a model to predict how fish assemblages characteristic of different stream types would change in response to decreased stream base flows. We describe model development and use in this case study. The model uses habitat suitability information (i.e., catchment size, base‐flow yield, and July mean water temperature) for over 40 fish species to predict assemblage structure in an individual river segment under a range of base‐flow reductions. By synthesizing model runs for individual fish species at representative segments for each of Michigan’s 11 ecological stream types, we developed curves describing how typical fish assemblages in each type respond to flow reduction. Each stream type‐specific, fish response curve was used to identify streamflow reduction levels resulting in adverse resource impacts to characteristic fish populations, the regulatory standard. Used together with a statewide map of stream types, our model provided a spatially comprehensive framework for evaluating impacts of flow withdrawals on biotic communities across a diverse regional landscape.     

Comparison of Three Pebble Count Protocols (EMAP,PIBO, and SFT) in Two Mountain Gravel‐Bed Streams1

Abstract: Although the term ``pebble count'' is in widespread use, there is no standardized methodology used for the field application of this procedure. Each pebble count analysis is the product of several methodological choices, any of which are capable of influencing the final result. Because there are virtually countless variations on pebble count protocols, the question of how their results differ when applied to the same study reach is becoming increasingly important. This study compared three pebble count protocols: the reach‐averaged Environmental Monitoring and Assessment Program (EMAP) protocol named after the EMAP developed by the Environmental Protection Agency, the habitat‐unit specific U.S. Forest Service’s PACFISH/INFISH Biological Opinion (PIBO) Effectiveness Monitoring Program protocol, and a data‐intensive method developed by the authors named Sampling Frame and Template (SFT). When applied to the same study reaches, particle‐size distributions varied among the three pebble count protocols because of differences in sample locations within a stream reach and along a transect, in particle selection, and particle‐size determination. The EMAP protocol yielded considerably finer, and the PIBO protocol considerably coarser distributions than the SFT protocol in the pool‐riffle study streams, suggesting that the data cannot be used interchangeably. Approximately half of the difference was due to sampling at different areas within the study reach (i.e., wetted width, riffles, and bankfull width) and at different locations within a transect. The other half was attributed to using different methods for particle selection from the bed, particle‐size determination, and the use of wide, nonstandard size classes. Most of the differences in sampling outcomes could be eliminated by using simple field tools, by collecting a larger sample size, and by systematically sampling the entire bankfull channel and all geomorphic units within the reach.     

Bed Stability and Sedimentation Associated With Human Disturbances in Pacific Northwest Streams1

Abstract: To evaluate anthropogenic sedimentation in United States (U.S.) Pacific Northwest coastal streams, we applied an index of relative bed stability (LRBS*) to summer low flow survey data collected using the U.S. Environmental Protection Agency’s Environmental Monitoring and Assessment Program field methods in a probability sample of 101 wadeable stream reaches. LRBS* is the log of the ratio of bed surface geometric mean particle diameter (D_gm) to critical diameter (D*_cbf) at bankfull flow, based on a modified Shield’s criterion for incipient motion. We used a formulation of LRBS* that explicitly accounts for reductions in bed shear stress that result from channel form roughness due to pools and wood. LRBS* ranged from ?1.9 to +0.5 in streams within the lower quartile of human riparian and basin disturbance, and was substantially lower (?4.2 to ?1.1) in streams within the upper quartile of human disturbance. Modeling results suggest that the expected range of LRBS* in streams without human disturbances in this region might be generally between ?0.7 and +0.5 in either sedimentary or volcanic lithology. However, streams draining relatively soft, erodible sedimentary lithology showed greater reductions in LRBS* associated with disturbance than did those having harder, more resistant volcanic (basalt) lithology with similar levels of basin and riparian disturbance. At any given level of disturbance, smaller streams had lower LRBS* than those with larger drainages. In sedimentary lithology (sandstone and siltstone), high‐gradient streams had higher LRBS* than did low‐gradient streams of the same size and level of human disturbance. High gradient streams in volcanic lithology, in contrast, had lower LRBS* than low‐gradient streams of similar size and disturbance. Correlations between D_gm and land disturbance were stronger than those observed between D*_cbf and land disturbance. This pattern suggests that land use has augmented sediment supplies and increased streambed fine sediments in the most disturbed streams. However, we also show evidence that some of the apparent reductions in LRBS*, particularly in steep streams draining small volcanic drainages, may have resulted in part from anthropogenic increases in bed shear stress. The synoptic survey methods and designs we use appear adequate to evaluate regional patterns in bed stability and sedimentation and their general relationship to human disturbances. More precise field measurements of channel slope, cross‐section geometry, and bed surface particle size would be required to use LRBS* in applications requiring a higher degree of accuracy and precision, such as site‐specific assessments at individual streams.     

Linking Hydrologic Alteration to Biological Impairment in Urbanizing Streams of the Puget Lowland,Washington, USA1

Abstract: We used a retrospective approach to identify hydrologic metrics with the greatest potential for ecological relevance for use as resource management tools (i.e., hydrologic indicators) in rapidly urbanizing basins of the Puget Lowland. We proposed four criteria for identifying useful hydrologic indicators: (1) sensitive to urbanization consistent with expected hydrologic response, (2) demonstrate statistically significant trends in urbanizing basins (and not in undeveloped basins), (3) be correlated with measures of biological response to urbanization, and (4) be relatively insensitive to potentially confounding variables like basin area. Data utilized in the analysis included gauged flow and benthic macroinvertebrate data collected at 16 locations in 11 King County stream basins. Fifteen hydrologic metrics were calculated from daily average flow data and the Pacific Northwest Benthic Index of Biological Integrity (B‐IBI) was used to represent the gradient of response of stream macroinvertebrates to urbanization. Urbanization was represented by percent Total Impervious Area (%TIA) and percent urban land cover (%Urban). We found eight hydrologic metrics that were significantly correlated with B‐IBI scores (Low Pulse Count and Duration; High Pulse Count, Duration, and Range; Flow Reversals, T_Qmean, and R‐B Index). Although there appeared to be a great deal of redundancy among these metrics with respect to their response to urbanization, only two of the metrics tested – High Pulse Count and High Pulse Range – best met all four criteria we established for selecting hydrologic indicators. The increase in these high pulse metrics with respect to urbanization is the result of an increase in winter high pulses and the occurrence of high pulse events during summer (increasing the frequency and range of high pulses), when practically none would have occurred prior to development. We performed an initial evaluation of the usefulness of our hydrologic indicators by calculating and comparing hydrologic metrics derived from continuous hydrologic simulations of selected basin management alternatives for Miller Creek, one of the most highly urbanized basins used in our study. We found that the preferred basin management alternative appeared to be effective in restoring some flow metrics close to simulated fully forested conditions (e.g., T_Qmean), but less effective in restoring other metrics such as High Pulse Count and Range. If future research continues to support our hypothesis that the flow regime, particularly High Pulse Count and Range, is an important control of biotic integrity in Puget Lowland streams, it would have significant implications for stormwater management.     

Observations and Modeling of Stream Plunging in an Urban Lake1

Owens, Emmet M., Steven W. Effler, Anthony R. Prestigiacomo, David A. Matthews, and Susan M. O’Donnell, 2012. Observations and Modeling of Stream Plunging in an Urban Lake. Journal of the American Water Resources Association (JAWRA) 48(4): 707‐721. DOI: 10.1111/j.1752‐1688.2012.00646.x Abstract: The plunging behavior of two tributaries in Onondaga Lake, New York, is quantified based on a program of monitoring, process studies, and modeling. The dynamics of buoyancy of the tributaries are resolved with hourly measurements of temperature (T), specific conductance (SC), and turbidity (Tn) at the mouths, and observations every 6 h in the lake. Negative buoyancy of the tributaries is found to diminish and change rapidly during runoff events compared to dry periods. In‐lake patterns of the transport of plunging inflow are resolved for dry weather conditions using a dye tracer, and following a runoff event through measurements of T, SC, and Tn. The hydrodynamic/transport model ELCOM (Estuary Lake and Coastal Ocean Model) is demonstrated to perform well in simulating these patterns. Analyses conducted with the model establish the importance of diurnal effects and in‐lake mixing mediated by wind, the need for temporally detailed measurements during runoff events, and modifications of the plunging behavior of the urban tributary as it passes through a harbor. The model provides critical information to support rehabilitation programs for the lake by quantifying the transport of the two largest tributaries, particularly the distribution of the loads between the upper waters and stratified layers. The model predicts that 10% of the urban tributary load enters the upper waters of the lake within 24 h for a dry weather period; this portion increases to 30% for a runoff event.     

Development and Comparison of Multiple Regression Models to Predict Bankfull Channel Dimensions for Use in Hydrologic Models

Channel dimensions are important input variables for many hydrologic models. As measurements of channel geometry are not available in most watersheds, they are often predicted using bankfull hydraulic geometry relationships. This study aims at improving existing equations that relate bankfull width, depth, and cross‐sectional area to drainage area (DA) without limiting their use to well‐gauged watersheds. We included seven additional variables in the equations that can be derived from data that are generally required by hydrologic models anyway and conducted several multiple regression analyses to identify the ideal combination of additional variables for nationwide and regional models for each Physiographic Division of the United States (U.S.). Results indicate that including the additional variables in the regression equations generally improves predictions considerably. The selection of relevant variables varies by Physiographic Division, but average annual precipitation (PCP) and temperature (TMP) were generally found to improve the models the most. Therefore, we recommend using regression equations with three independent variables (DA, PCP, and TMP) to predict bankfull channel dimensions for hydrologic models. Furthermore, we recommend using the regional equations for watersheds within regions from which data were used for model development, whereas in all other parts of the U.S. and the rest of the world, the nationwide equations should be given preference.