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We describe a general process for developing an index of fish assemblage integrity, using the Willamette Valley of Oregon, U.S.A., as an example. Such an index is useful for assessing the effects of humans on entire fish assemblages, and the general process can be applied to any biological assemblage and any region. First, a reference condition was determined from historical information, and then candidate metrics of ecological importance were listed. The variability of the candidate metrics in time and space was estimated and their responsiveness to independent measures of riparian and stream habitat quality assessed. Metrics were scored continuously from 0 to 10, producing an index of biological integrity (IBI) that was weighted to range from 0 to 100 regardless of the number of metrics. The index, developed from a set of 35 sites, was then tested on an independent set of eight urban sites sampled by the Oregon Department of Fish and Wildlife. Thirteen of the 16 candidate metrics were appropriate and produced an IBI with among-site variance triple that of revisit variance. The method distinguished sites with acceptable fish assemblages from marginally and severely impaired sites.

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We assessed the effects of nonnative fish on native fish biodiversity, using assemblage data collected during 1991-1996 from 203 randomly selected lakes in the northeastern USA by the Environmental Monitoring and Assessment Program (EMAP) of the U.S. Environmental Protection Agency. An estimated 74% (Ϯ17.6%, 95% confidence interval) of the region's 10,608 lakes between 1 and 10,000 ha contain at least one introduced species. Based on our samples, nonnative individuals outnumbered natives in an estimated 31.5% (Ϯ11%) of lakes. Regression models indicated that native, introduced, and total species richness were associated with lake surface area, elevation, and lake depth (0.31 Յ R 2 Յ 0.81). The intensity of human disturbance in the watershed was positively associated with introduced species richness but not associated with native species richness. The number of nonnative species was a significant variable in the native-species regression models for the entire Northeast and for only one of five subregions, the Northeast Coastal Zone ecoregion. Of the types of fishes that have been introduced, littoral predators-primarily Micropterus-appeared to have the greatest negative effect on native species richness. Small or soft-finned species appeared to be the least tolerant of these introduced predators. Native brook trout and minnow assemblages, typical of northern lakes in the Northeast but now rare in the Adirondacks, appeared to be at the greatest risk from continued introductions in northeastern New England. Current among-lake (␤) species diversity was associated more with regional diversity of lake types than with extent or dominance of nonnative species. Without quantitative historical data, it was not possible to demonstrate a homogenizing effect of introductions on lake fish assemblages.