Are Toronto’s streams sick? A look at the fish and benthic invertebrate communities in the Toronto region in relation to the urban stream syndrome

Impacts of urbanization on aquatic ecosystems are intensifying as urban sprawl spreads across the global land base. The urban stream syndrome (USS) identifies “symptoms” associated with urban development including changes in biotic communities, hydrology, water chemistry, and channel morphology. Direct relationships between road density (as surrogate of urbanization) and indicators of the USS were identified for streams in the Toronto region. Significant negative relationships were revealed between road density and biological (fish and benthic macroinvertebrate) richness, diversity, and fish Index of Biotic Integrity scores. Significant positive relationships were found between road density and tolerant fish/benthic macroinvertbrates, benthos Family Biotic Index scores, mean summer stream temperature, stream flashiness, and several water quality variables. Analysis of biological data showed that only four fish species and a reduced number of benthic macroinvertebrate families remained at the most urbanized sites. Road density was found to be a major determinant in both the fish and benthic macroinvertebrate community structure.     

Land use impacts on river health of Uma Oya,Sri Lanka: implications of spatial scales

Human actions on landscapes are a principal threat to the ecological integrity of river ecosystems worldwide. Tropical landscapes have been poorly investigated in terms of the impact of catchment land cover alteration on water quality and biotic indices in comparison to temperate landscapes. Effects of land cover in the catchment at two spatial scales (catchment and site) on stream physical habitat quality, water quality, macroinvertebrate indices and community composition were evaluated for Uma Oya catchment in the upper Mahaweli watershed, Sri Lanka. The relationship between spatial arrangement of land cover in the catchment and water quality, macroinvertebrate indices and community composition was examined using univariate and multivariate approaches. Results indicate that chemical water quality variables such as conductivity and total dissolved solids are mostly governed by the land cover at broader spatial scales such as catchment scale. Shannon diversity index was also affected by catchment scale forest cover. In stream habitat features, nutrients such as N-NO₃ ^?, macroinvertebrate family richness, %shredders and macroinvertebrate community assemblages were predominantly influenced by the extent of land cover at 200 m site scale suggesting that local riparian forest cover is important in structuring macroinvertebrate communities. Thus, this study emphasizes the importance of services provided by forest cover at catchment and site scale in enhancing resilience of stream ecosystems to natural forces and human actions. Findings suggest that land cover disturbance effects on stream ecosystem health could be predicted when appropriate spatial arrangement of land cover is considered and has widespread application in the management of tropical river catchments.     

Visually determined stream mesohabitats influence benthic macroinvertebrate assessments in headwater streams

Mesohabitat components such as substrate and surface flow types are intimately related to benthic macroinvertebrate assemblages in streams. Visual assessments of the distribution of these components provide a means of evaluating physical habitat heterogeneity and aid biodiversity surveys and monitoring. We determined the degree to which stream site and visually assessed mesohabitat variables explain variability (i.e., beta-diversity) in the relative abundance and presence-absence of all macroinvertebrate families and of Ephemeroptera, Plecoptera, and Trichoptera (EPT) genera. We systematically sampled a wide variety of mesohabitat arrangements as they occured in stream sites. We also estimated how much of the explanation given by mesohabitat was associated with substrate or surface flow types. We performed variation partitioning to determine fractions of explained variance through use of partial redundancy analysis (pRDA). Mesohabitats and stream sites explained together from 23 to 32 % of the variation in the four analyses. Stream site explained 8–11 % of that variation, and mesohabitat variables explained 13–20 %. Surface flow types accounted for >60 % of the variation provided by the mesohabitat component. These patterns are in accordance with those obtained in previous studies that showed the predominance of environmental variables over spatial location in explaining macroinvertebrate distribution. We conclude that visually assessed mesohabitat components are important predictors of assemblage composition, explaining significant amounts of beta-diversity. Therefore, they are critical to consider in ecological and biodiversity assessments involving macroinvertebrates.     

Relationships of sedimentation and benthic macroinvertebrate assemblages in headwater streams using systematic longitudinal sampling at the reach scale

Investigating relationships of benthic invertebrates and sedimentation is challenging because fine sediments act as both natural habitat and potential pollutant at excessive levels. Determining benthic invertebrate sensitivity to sedimentation in forested headwater streams comprised of extreme spatial heterogeneity is even more challenging, especially when associated with a background of historical and intense watershed disturbances that contributed unknown amounts of fine sediments to stream channels. This scenario exists in the Chattahoochee National Forest where such historical timber harvests and contemporary land-uses associated with recreation have potentially affected the biological integrity of headwater streams. In this study, we investigated relationships of sedimentation and the macroinvertebrate assemblages among 14 headwater streams in the forest by assigning 30, 100-m reaches to low, medium, or high sedimentation categories. Only one of 17 assemblage metrics (percent clingers) varied significantly across these categories. This finding has important implications for biological assessments by showing streams impaired physically by sedimentation may not be impaired biologically, at least using traditional approaches. A subsequent multivariate cluster analysis and indicator species analysis were used to further investigate biological patterns independent of sedimentation categories. Evaluating the distribution of sedimentation categories among biological reach clusters showed both within-stream variability in reach-scale sedimentation and sedimentation categories generally variable within clusters, reflecting the overall physical heterogeneity of these headwater environments. Furthermore, relationships of individual sedimentation variables and metrics across the biological cluster groups were weak, suggesting these measures of sedimentation are poor predictors of macroinvertebrate assemblage structure when using a systematic longitudinal sampling design. Further investigations of invertebrate sensitivity to sedimentation may benefit from assessments of sedimentation impacts at different spatial scales, determining compromised physical habitat integrity of specific taxa and developing alternative streambed measures for quantifying sedimentation.     

Testing Bioassessment Metrics: Macroinvertebrate, Sculpin, and Salmonid Responses to Stream Habitat, Sediment, and Metals

The purpose of this article is to report on the testing of responses of multimetric macroinvertebrate and habitat indices to common disturbances to streams: stream habitat alteration, excessive sediment, and elevated metals concentrations. Seven macroinvertebrate community metrics were combined into a macroinvertebrate biotic index (MBI), and 11 channel morphology, riparian, and substrate features were combined into a habitat index. Indices were evaluated by comparing the habitat results to fish population surveys and comparing the macroinvertebrate results to habitat ratings, percent fine sediments measured by Wolman pebble counts, and copper concentrations. Macroinvertebrate scores decreased with increasing percentages of fine sediments measured either across the bankfull or instream channel widths. Macroinvertebrate scores decreased with increasing copper. One metric, richness of Ephemeroptera, Plecoptera, and Trichoptera (EPT) taxa, was more responsive to both copper and sediment than was the multimetric MBI. Habitat scores corresponded well with the age class structure of salmonids, but not with that of benthic sculpins. Both salmonid and sculpin age classes declined with increasing percentages of fine sediments. The decline was graded with the sculpin age classes, whether fine sediments were measured across the instream or bankfull channel, whereas salmonids consistently responded only to the instream fine sediments.     

Influence of Riffle and Snag Habitat Specific Sampling on Stream Macroinvertebrate Assemblage Measures in Bioassessment

Stream macroinvertebrate communities vary naturally among types of habitats where they are sampled, which affects the results of environmental assessment. We analyzed macroinvertebrates collected from riffle and snag habitats to evaluate influences of habitat-specific sampling on taxon occurrence, assemblage measures, and biotic indices. We found considerably more macroinvertebrate taxa unique to snags (143 taxa) than to riffles (75 taxa), and the numbers of taxa found in both riffles and snags (149 taxa) were similar to that found in snags. About 64% of the 47 macroinvertebrate measures we tested differed significantly between riffles and snags. Eighty percent intercepts of regressions between biotic indices and urban or agricultural land uses differed significantly between riffles and snags. The Hilsenhoff biotic index calculated from snag samples explained 69% of the variance of riffle samples and classified 66% of the sites into the same stream health group as the riffle samples. However, four multimetric indices for snag samples explained less than 50% of the variance of riffle samples and classified less than 50% of the sites into the same health group as the riffle samples. We concluded that macroinvertebrate indices developed for riffle/run habitat should not be used for snag samples to assess stream impairment. We recommend developing an index of biotic integrity specifically for snags and using snags as an alternate sampling substrate for streams that naturally lack riffles.     

Advantages of Geographically Weighted Regression for Modeling Benthic Substrate in Two Greater Yellowstone Ecosystem Streams

Stream habitat assessments are commonplace in fish management, and often involve nonspatial analysis methods for quantifying or predicting habitat, such as ordinary least squares regression (OLS). Spatial relationships, however, often exist among stream habitat variables. For example, water depth, water velocity, and benthic substrate sizes within streams are often spatially correlated and may exhibit spatial nonstationarity or inconsistency in geographic space. Thus, analysis methods should address spatial relationships within habitat datasets. In this study, OLS and a recently developed method, geographically weighted regression (GWR), were used to model benthic substrate from water depth and water velocity data at two stream sites within the Greater Yellowstone Ecosystem. For data collection, each site was represented by a grid of 0.1 m² cells, where actual values of water depth, water velocity, and benthic substrate class were measured for each cell. Accuracies of regressed substrate class data by OLS and GWR methods were calculated by comparing maps, parameter estimates, and determination coefficient r ². For analysis of data from both sites, Akaike’s Information Criterion corrected for sample size indicated the best approximating model for the data resulted from GWR and not from OLS. Adjusted r ² values also supported GWR as a better approach than OLS for prediction of substrate. This study supports GWR (a spatial analysis approach) over nonspatial OLS methods for prediction of habitat for stream habitat assessments.     

Heavy metals fractionation in surface sediments of Gowatr bay-Iran

Establishing the effectiveness of habitat features to act as surrogate measures of diversity and abundance of juvenile reef fish provides information that is critical to coral reef management. When accurately set on a broader spatial context, microhabitat information becomes more meaningful and its management application becomes more explicit. The goal of the study is to identify coral reef areas potentially important to juvenile fishes in Ngederrak Reef, Republic of Palau, across different spatial scales. To achieve this, the study requires the accomplishment of the following tasks: (1) structurally differentiate the general microhabitat types using acoustics; (2) quantify microhabitat association with juvenile reef fish community structure; and (3) conduct spatial analysis of the reef-wide data and locate areas optimal for juvenile reef fish settlement. The results strongly suggest the importance of branching structures in determining species count and abundance of juvenile reef fish at the outer reef slope of Ngederrak Reef. In the acoustic map, the accurate delineation of these features allowed us to identify reef areas with the highest potential to harbor a rich aggregation of juvenile reef fish. Using a developed spatial analysis tool that ranks pixel groups based on user-defined parameters, the reef area near the Western channel of Ngederrak is predicted to have the most robust aggregation of juvenile reef fish. The results have important implications not only in management, but also in modeling the impacts of habitat loss on reef fish community. At least for Ngederrak Reef, the results advanced the utility of acoustic systems in predicting spatial distribution of juvenile fish.     

Effects of geomorphology, habitat, and spatial location on fish assemblages in a watershed in Ohio, USA

In this paper, we evaluate relationships between in-stream habitat, water chemistry, spatial distribution within a predominantly agricultural Midwestern watershed and geomorphic features and fish assemblage attributes and abundances. Our specific objectives were to: (1) identify and quantify key environmental variables at reach and system wide (watershed) scales; and (2) evaluate the relative influence of those environmental factors in structuring and explaining fish assemblage attributes at reach scales to help prioritize stream monitoring efforts and better incorporate all factors that influence aquatic biology in watershed management programs. The original combined data set consisted of 31 variables measured at 32 sites, which was reduced to 9 variables through correlation and linear regression analysis: stream order, percent wooded riparian zone, drainage area, in-stream cover quality, substrate quality, gradient, cross-sectional area, width of the flood prone area, and average substrate size. Canonical correspondence analysis (CCA) and variance partitioning were used to relate environmental variables to fish species abundance and assemblage attributes. Fish assemblages and abundances were explained best by stream size, gradient, substrate size and quality, and percent wooded riparian zone. Further data are needed to investigate why water chemistry variables had insignificant relationships with IBI scores. Results suggest that more quantifiable variables and consideration of spatial location of a stream reach within a watershed system should be standard data incorporated into stream monitoring programs to identify impairments that, while biologically limiting, are not fully captured or elucidated using current bioassessment methods.     

Limitations of habitats as biodiversity surrogates for conservation planning in estuaries

Increasing pressures on global biodiversity and lack of data on the number and abundance of species have motivated conservation planners and researchers to use more readily available information as proxies or surrogates for biodiversity. “Habitat” is one of the most frequently used surrogates but its assumed value in marine conservation planning is not often tested. The present study developed and tested three alternative habitat classification schemes of increasing complexity for a large estuary in south-east Australia and tested their effectiveness in predicting spatial variation in macroinvertebrate biodiversity and selecting estuarine protected areas to represent species. The three habitat classification schemes were: (1) broad-scale habitats (e.g., mangroves and seagrass), (2) subdivision of each broad-scale habitat by a suite of environmental variables that varied significantly throughout the estuary, and (3) subdivision of each broad-scale habitat by the subset of environmental variables that best explained spatial variation in macroinvertebrate biodiversity. Macroinvertebrate assemblages differed significantly among the habitats in each classification scheme. For each classification scheme, habitat richness was significantly correlated with species richness, total density of macroinvertebrates, assemblage dissimilarity, and summed irreplaceability. However, in a reserve selection process designed to represent examples of each habitat, no habitat classification scheme represented species significantly better than a random selection of sites. Habitat classification schemes may represent variation in estuarine biodiversity; however, the results of this study suggest they are inefficient in designing representative networks of estuarine protected areas.     

Local physical habitat quality cloud the effect of predicted pesticide runoff from agricultural land in Danish streams

The combination of intensive agricultural activities and the close connectivity between land and stream emphasise the potential risk of pesticide exposure in Danish streams. Benthic macroinvertebrates are applied in the assessment of stream ecological status, and some sensitive species have been shown to respond strongly to brief pulses of pesticide contamination. In this study we investigate the impact of agriculturally derived pesticides on stream macroinvertebrate communities in Denmark. As a measure of toxic pressure we apply the Runoff Potential. We investigated a total of 212 streams. These were grouped into distinct classes according to the magnitude of pesticide contamination in the period from 2003-2006. A total of 24 different macroinvertebrate indices were applied to detect effects of pesticide runoff (e.g. the SPEAR-index and the number of EPT taxa). We found high predicted pesticide runoff in 39% of the streams, but we found no significant effect of predicted pesticide exposure on stream macroinvertebrate indices. We, additionally, examined the influence of a series of environmental parameters ranging from site scale to catchment scale on the macroinvertebrate community. Relative proportions of gravel, sand and silt in bed sediments explained most of the variation in macroinvertebrate indices as well as the upstream riparian habitat quality. We suggest that the Runoff Potential model overestimate pesticide runoff contamination in Danish streams due the presence of buffer strips enforced by Danish legislation. When pesticide runoff contamination is low to moderate, poor physical properties (indirectly related to agricultural activity) are the main impediment for the ecological quality of Danish streams.     

Review of the effects of in-stream pipeline crossing construction on aquatic ecosystems and examination of Canadian methodologies for impact assessment

Pipeline crossing construction alters river and stream channels, hence may have detrimental effects on aquatic ecosystems. This review examines the effects of crossing construction on fish and fish habitat in rivers and streams, and recommends an approach to monitoring and assessment of impacts associated with these activities. Pipeline crossing construction is shown to not only compromise the integrity of the physical and chemical nature of fish habitat, but also to affect biological habitat (e.g., benthic invertebrates and invertebrate drift), and fish behavior and physiology. Indicators of effect include: water quality (total suspended solids TSS), physical habitat (substrate particle size, channel morphology), benthic invertebrate community structure and drift (abundance, species composition, diversity, standing crop), and fish behavior and physiology (hierarchy, feeding, respiration rate, loss of equilibrium, blood hematocrit and leukocrit levels, heart rate and stroke volume). The Before-After-Control-Impact (BACI) approach, which is often applied in Environmental Effects Monitoring (EEM), is recommended as a basis for impact assessment, as is consideration of site-specific sensitivities, assessment of significance, and cumulative effects.     

Assessment of wadeable stream resources in the driftless area ecoregion in Western Wisconsin using a probabilistic sampling design

The Wisconsin Department of Natural Resources (WDNR), with support from the U.S. EPA, conducted an assessment of wadeable streams in the Driftless Area ecoregion in western Wisconsin using a probabilistic sampling design. This ecoregion encompasses 20% of Wisconsin’s land area and contains 8,800 miles of perennial streams. Randomly-selected stream sites (n = 60) equally distributed among stream orders 1–4 were sampled. Watershed land use, riparian and in-stream habitat, water chemistry, macroinvertebrate, and fish assemblage data were collected at each true random site and an associated “modified-random” site on each stream that was accessed via a road crossing nearest to the true random site. Targeted least-disturbed reference sites (n = 22) were also sampled to develop reference conditions for various physical, chemical, and biological measures. Cumulative distribution function plots of various measures collected at the true random sites evaluated with reference condition thresholds, indicate that high proportions of the random sites (and by inference the entire Driftless Area wadeable stream population) show some level of degradation. Study results show no statistically significant differences between the true random and modified-random sample sites for any of the nine physical habitat, 11 water chemistry, seven macroinvertebrate, or eight fish metrics analyzed. In Wisconsin’s Driftless Area, 79% of wadeable stream lengths were accessible via road crossings. While further evaluation of the statistical rigor of using a modified-random sampling design is warranted, sampling randomly-selected stream sites accessed via the nearest road crossing may provide a more economical way to apply probabilistic sampling in stream monitoring programs.     

Monitoring and estimating scale-dependent hierarchical relationships between Sicyopterus japonicus density and stream habitat features in different seasons in northern Taiwan

Biological and physical processes operate collaboratively through spatial or temporal scales to form ecological patterns, which are considered as a key element for understanding the natural liens within an ecosystem. Given the importance of scaling in ecological inference, this study elucidates how physical and biological variables under or within scales interact with each other. Density of Sicyopterus japonicus and environmental variables are examined and quantified at 70 stream sections distributed among 14 reaches in the Datuan stream catchment of northern Taiwan during the fall and winter of 2007, as well as the spring and summer of 2008. Hierarchical linear regression analysis indicates that S. japonicus density and habitat features are related on two levels, i.e., sections within reaches and reaches within streams throughout the year. Moreover, parameter uncertainty is represented by the confidence interval, which is calculated by the variance-covariance matrix of hierarchical linear model (HLM) parameters. According to HLM results, environmental variables at the section level (water depth and current velocity) and the reach level (stream width, water temperature, stream slope, soil erosion index) influence S. japonicus density. Although S. japonicus density varies significantly among reaches and sections within reaches, cross-level interaction may not always influence the distribution, processes and activities of S. japonicus throughout the year. The HLMs of S. japonicus density associated with stream features describe thoroughly multiple processes and the activities of S. japonicus across scales and within scales during different seasons. The annual HLM results represent the overall biological and physical patterns of the Datuan stream annually, explaining why they do not reflect seasonal associations or explain S. japonicus-related activities and environmental features of the stream.     

Maryland Biological Stream Survey: A State Agency Program to Assess the Impact of Anthropogenic Stresses on Stream Habitat Quality and Biota

The Maryland Department of Natural Resources is conducting the Maryland Biological Stream Survey, a probability-based sampling program, stratified by river basin and stream order, to assess water quality, physical habitat, and biological conditions in first through third order, non-tidal streams. These streams comprise about 90% of all lotic water miles in the state. About 300 sites (75 m segments) are being sampled during spring and summer each year. All basins in the state will be sampled over a three-year period, 1995-97. MBSS developments in 1995-96 included (1) an electrofishing capture efficiency correction method to improve the accuracy of fish population estimates, (2) two indices of biotic integrity (IBI) for fish assemblages to identify degraded streams, and (3) land use information for catchments upstream of sampled sites to investigate associations between stream condition and anthropogenic stresses. Based on fish IBI scores at 270 stream sites in six basins sampled in 1995, 11% of non-tidal stream miles in Maryland were classified as very poor, 15% as poor, 24% as fair, and 27% as good. IBIs have not yet been developed for stream sites with catchment areas less than 120 hectares (23% of non-tidal stream miles). IBI scores declined with stream acid neutralizing capacity (ANC) and pH, an association that was also evident for fish species richness, biomass, and density. Low IBI scores were associated with several measures of degraded stream habitat, but not with local riparian buffer width. There was a significant negative association between IBI scores and urban land use upstream of sampled sites in the only extensively urbanized basin assessed in 1995. Future plans for the MBSS include (1) identifying all benthic macroinvertebrate samples to genus, (2) developing benthic macroinvertebrate, herpetofaunal, and physical habitat indicators, and (3) enhancing the analysis of stream condition-stressor associations by refining landscape metrics and using multi-variate techniques.     

Spatial heterogeneity of stream environmental conditions and macroinvertebrates community in an agriculture dominated watershed and management implications for a large river (the Liao River,China) basin

Understanding the effects of watershed land uses (e.g., agriculture, urban industry) on stream ecological conditions is important for the management of large river basins. A total of 41 and 56 stream sites (from first to fourth order) that were under a gradient of watershed land uses were monitored in 2009 and 2010, respectively, in the Liao River Basin, Northeast China. The monitoring results showed that a total of 192 taxa belonging to four phyla, seven classes, 21 orders and 91 families were identified. The composition of macroinvertebrate community in the Liao River Basin was dominated by aquatic insect taxa (Ephemeroptera and Diptera), Oligochaeta and Molluscs. The functional feeding group GC (Gatherer/Collector) was dominant in the whole basin. Statistical results showed that sites with less watershed impacts (lower order sites) were characterized by higher current velocity and habitat score, more sensitive taxa (e.g., Ephemeroptera), and the substrate was dominated by high percentage of cobble and pebble. The sites with more impacts from agriculture and urban industry (higher order sites) were characterized by higher biochemical (BOD₅) and chemical oxygen demand (COD), more tolerant taxa (e.g., Chironominae), and the substrate was dominated by silt and sand. Agriculture and urban-industry activities have reduced habitat condition, increased organic pollutants, reduced macroinvertebrate abundance, diversity, and sensitive taxa in streams of the lower Liao River Basin. Restoration of degraded habitat condition and control of watershed organic pollutants could be potential management priorities for the Basin.     

Hydrologic disturbance reduces biological integrity in urban streams

The impact of urbanization on stream ecosystems is linked by land cover changes to the alteration of the natural hydrology and subsequent physical disruption of stream biota and habitat. Seasonal floods are part of the natural disturbance regime of many streams, but urbanization increases their frequency and magnitude. This study evaluated the impact of hydrologic disturbance on fish and aquatic macroinvertebrates in 81 (56 urban/25 reference) Ohio streams. Hydrologic variables included annual and monthly 24-h rainfall maxima and computed annual peak discharge, with computation supported by GIS-based drainage area delineation and land cover characterization. Ohio biological criteria for fish and macroinvertebrates measured during the late spring and summer were negatively impacted by annual peak discharge in urban streams as compared to reference streams. Results support the application of stormwater best management practices as part of stream restoration efforts to mitigate urbanization impacts to fish and macroinvertebrates.     

Relations between macroinvertebrates, nutrients, and water quality criteria in wadeable streams of Maryland, USA

In an ongoing effort to propose biologically protective nutrient criteria, we examined how total nitrogen (TN) and its forms were associated with macroinvertebrate communities in wadeable streams of Maryland. Taxonomic and functional metrics of an index of biological integrity (IBI) were significantly associated with multiple nutrient measures; however, the highest correlations with nutrients were for ammonia-N and nitrite-N and among macroinvertebrate measures were for Beck’s Biotic Index and its metrics. Since IBI metrics showed comparatively less association, we evaluated how macroinvertebrate taxa related to proposed nutrient criteria previously derived for those same streams instead of developing nutrient–biology thresholds. We identified one tolerant and three intolerant taxa whose occurrence appeared related to a TN benchmark. Individually, these taxa poorly indicated whether streams exceeded the benchmark, but combining taxa notably improved classification rates. We then extracted major physiochemical gradients using principal components analysis to develop models that assessed their influence on nutrient indicator taxa. The response of intolerant taxa was predominantly influenced by a nutrient-forest cover gradient. In contrast, habitat quality had a greater effect on tolerant taxa. When taxa were aggregated into a nutrient sensitive index, the response was primarily influenced by the nutrient-forest gradient. Multiple lines of evidence highlight the effects of excessive nutrients in streams on macroinvertebrate communities and taxa in Maryland, whose loss may not be reflected in metrics that form the basis of biological criteria. Refinement of indicator taxa and a nutrient-sensitive index is warranted before thresholds in aquatic life to water quality are quantified.     

Relation of fish and shellfish distributions to habitat and water quality in the Mobile Bay estuary, USA

The Mobile Bay estuary in the northern Gulf of Mexico provides a rich habitat for many fish and shellfish, including those identified as economically and ecologically important. The National Estuary Program in Mobile Bay has focused on restoration of degraded estuarine habitat on which these species depend. To support this effort, we used statistical techniques of ordination, cluster analysis, and discriminant analysis to relate distributions of individual fish and shellfish species and species assemblages to two dozen water quality and habitat variables in a geo-referenced database. Species appeared to respond to dominant gradients of low to high salinity and upland to offshore habitat area; many of the 15 communities identified via cluster analysis showed aggregated spatial distributions that could be related to habitat characteristics. Species in the Mobile River Delta were distinct from those in other areas of the estuary. This analysis supports habitat management in the Mobile Bay estuary; however, due to mobility of organisms among sampling locations and the dynamic environmental conditions in estuaries, we conclude that the analyses presented here are most appropriate for an evaluation of the estuary as a whole.