We developed a modified index of biotic integrity (IBI) for the Tallapoosa River system based on small-bodied fishes. The modified IBI comprised 9 metrics in 4 categories: (1) species richness and composition, (2) indicator species, (3) trophic function, and (4) abundance. We used distribution records and collection data from 1990-1995 to derive expected values for metrics. The IBI was most sensitive to changes in percentage of insectivorous cyprinids, percentage of intolerant species, fish abundance, and number of darter species, and least sensitive to total species richness. IBI scores generally were lower at sites experiencing more severe flow fluctuations as a result of hydropeaking dam operation. We recommend that the IBI be further tested, refined, and used as part of long-term monitoring programs in regulated southeastern river systems.