We used fish assemblage data collected by daytime electrofishing during 1996-1999 from 155 main-channel-border sites on 30 large warmwater rivers in Wisconsin to construct, test, and apply an index of biotic integrity (IBI). Our goal was to develop an effective and rapid way to use fishes to as,ess the environmental quality of river ecosystems in the state. Fourteen sites were visited more than once for a total of 187 samples, 101 of which (randomly chosen) were used to develop the IBI and the remaining 86 to test it. Prior to sampling, sites were classified as "least impacted" or as affected by impoundments, daily "peaking" flows from hydropower dams, non-point-source pollution from the watershed, point source pollution from industrial and municipal discharges (within the last 35 years), or multiple human impacts. Of the 26 potential IBI metrics considered, 10 were chosen: the total weight of the catch (excluding tolerant species); the number of native, sucker, intolerant, or riverine specialist species. the percentage of the individuals captured that were deformed or diseased, riverine specialists, or simple lithophilous spawners; and the percentage of the total weight of the catch that were insectivores or round-bodied suckers. Six metrics had different scoring criteria for northern and southern Wisconsin. For both the test subset and the entire dataset. the least-impacted sites had significantly higher mean scores and lower temporal variation than the other site classifications, indicating that they had the best ecosystem quality. Multiple-impact and non-point-source sites had the lowest means and most variable scores, signifying degraded ecosystem quality. Impoundment and hydropower peaking sites had slightly but not significantly better scores. Peaking sites on river reaches that are highly fragmented by dams tended to have lower scores than peaking sites on relatively long (> 60 km), contiguous river reaches. Point source sites had significantly better scores than multiple-impact and non-point-source sites, indicating benefits to biotic integrity from recent treatment of municipal and industrial discharges.