Habitat and biological communities were sampled at 10 sites in the Great Salt Lake Basins as part of the U.S. Geological Survey National Water-Quality Assessment program to assess the occurrence and distribution of biological organisms in relation to environmental conditions. Sites were distributed among the Bear River, Weber River, and Utah Lake/Jordan River basins and were selected to represent stream conditions in different land-use settings that are prominent within the basins, including agriculture, rangeland, urban, and forested.

High-gradient streams had more diverse habitat conditions with larger substrates and more dynamic flow characteristics and were typically lower in discharge than low-gradient streams, which had a higher degree of siltation and lacked variability in geomorphic channel characteristics, which may account for differences in habitat. Habitat scores were higher at high-gradient sites with high percentages of forested land use within their basins. Sources and causes of stream habitat impairment included effects from channel modifications, siltation, and riparian land use. Effects of hydrologic modifications were evident at many sites.

Algal sites where colder temperatures, less nutrient enrichment, and forest and rangeland uses dominated the basins contained communities that were more sensitive to organic pollution, siltation, dissolved oxygen, and salinity than sites that were warmer, had higher degrees of nutrient enrichment, and were affected by agriculture and urban land uses. Sites that had high inputs of solar radiation and generally were associated with agricultural land use supported the greatest number of algal species.

Invertebrate samples collected from sites where riffles were the richest-targeted habitat differed in species composition and pollution tolerance from those collected at sites that did not have riffle habitat (nonriffle sites), where samples were collected in depositional areas, woody snags, or macrophyte beds. Invertebrate taxa richness, pollution tolerance, and trophic interactions at riffle and nonriffle sites responded differently to environmental variables.

Fish communities were assessed in relation to the designated beneficial use for aquatic life for each site. Fish-community sites in basins where agriculture and urbanization were prevalent consistently had poorer conditions than sites with forest and rangeland uses. Warm temperatures appear to be limiting most native fish species, and more introduced, warm-water fish species were present at sites with warmer temperatures. Ranges of environmental conditions where native species were present or absent were identified.

The farthest-upstream site in each of the three basins had better ecological condition overall, as indicated by the integrity of habitat and the presence of more sensitive algae, invertebrate, and fish species than were observed at sites downstream. The farthest-downstream site in each of the three basins showed the poorest ecological condition, with more tolerant organisms present, degraded habitat and water-quality conditions, and a high degree of effects from agriculture, grazing, and urbanization. Of the mid-basin sites, the site most affected by urbanization had more degraded biological condition than the agricultural indicator site of similar basin size.