The Index of Biotic Integrity (IBI) has proven to be an important assessment tool for evaluating the resource quality of aquatic ecosystems. We used a modified IBI for Great Rivers based on collections from the Wabash River in west-central Indiana. We evaluated natural, inherent variation in natural phenomena, gear effects and land use modification over a 20-year period. Sixty-three stations distributed through 260 km of river were sampled 2-3 times per year to evaluate fish community structure and function. Natural changes in variation included temporal variation, hydrologic cycle and recruitment. Our results suggest that removing gizzard shad, whose population levels fluctuate widely, from percentage metrics enhanced assessment and exposed subtle affects. IBI scores consistently declined in a downstream direction. IBI profiles based on numbers were almost always higher than those using biomass, but patterns corresponded well for both metric systems. Combining biomass catches by seining and electrofishing did not substantially change the observed patterns compared to numeric electrofishing catches. The large number of small species taken by seining overwhelmed the subtle patterns observed at least impacted stations, but greater departures in quality were evident at impaired downstream locations. Floods decimated fish communities throughout the river. Fish moved out of stressed areas during severe droughts and into areas near clean tributaries. Certain structured attributes of Great River fish communities showed statistically significant changes based on ecoregion scales. Total number of species, number of sensitive species, number of centrarchid species and percentage of simple lithophils declined between the Corn Belt Plain and Interior River Lowland ecoregions, but water quality factors might also be influential. These changes in metric attributes lowered IBI scores by 6-10 cumulative points.
