The lower Boise River, between Lucky Peak Dam and the mouth of the river near Parma, Idaho, is adversely affected by various land- and water-use activities. To assess the biotic integrity of the river and the effects of environmental perturbations on aquatic community structure, and to provide a baseline from which to identify future changes in habitat conditions, biological data were collected from October 1995 through January 1998 and evaluated using protocols developed for the U.S. Geological Survey National Water-Quality Assessment Program. Aquatic biological communities were sampled according to the following schedule: epilithic periphyton were collected in October 1995, October 1996, and August 1997; benthic macroinvertebrates were collected in October 1995, 1996, and 1997; and fish were collected in December 1996 and August 1997. Qualitative measurements of instream and riparian habitat indicated an overall decrease in instream habitat quality in a downstream direction. Embeddedness was high at all sites but was lower at the Eckert Road site than at the downstream sites near Middleton and Parma. Silt/sand substrate increased from 17 percent at the Eckert Road site to 49 percent near the mouth of the river. The Eckert Road site had a mix of geomorphic channel units (pool/riffle/run), whereas the Middleton and Parma sites were dominated by runs with very little pool or riffle habitat. Epilithic periphyton chlorophyll-a and ashfree dry weight values tended to increase downstream to the Middleton site and decrease from Middleton to the downstream sites near Caldwell and near Parma. Benthic index of biotic integrity (B-IBI) scores for macroinvertebrates collected in 1995, 1996, and 1997 were highest at the Eckert Road site and decreased at sites downstream. IBI scores for fish collected in 1996 were similar at the Glenwood Bridge and Middleton sites (17 and 16, respectively) and were indicative of a low to moderate level of disturbance. In contrast, the IBI score of 6 at the site near Parma was markedly lower and was indicative of more degraded conditions.
