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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.

We examined the sampling effort required in wadeable western Oregon streams at base flow to estimate fish species richness, percent abundance, and biotic integrity when employing three persons and one backpack electrofisher. Reaches were oversampled longitudinally and data were recorded separately for each habitat unit, allowing us to treat each habitat unit separately during data analyses. The median values of species richness from Monte Carlo simulations of the data indicated that a stream reach 40 times its mean wetted width was adequate to estimate 90% of species richness (i.e., all common species) in western Oregon fish assemblages. A reach length of 40 wetted channel widths was also adequate to precisely score an index of biotic integrity developed for western Oregon. However, where 40 channel widths are less than 150 m, we recommend a minimum distance of 150 m to ensure that sufficient numbers of individuals are captured, rare habitats are encountered, and riparian conditions do not fully determine channel morphology. In addition, at four sites we compared a rapid (4-h), one-pass sampling protocol of reaches 40 channel widths in length with an intensive, three-pass electrofishing protocol lasting more than 10 h. The rapid protocol occasionally underestimated species richness by missing vagile, cryptic, or rare species, but it usually estimated species richness, percent abundance, and the IBI as well as the intensive protocol. The rapid protocol and quantitative fish population estimates tracked the same trends in population size at one site for 5 years.