The Bayou Pierre system in western Mississippi is currently experiencing extensive erosion, with pulses of erosion moving from lower to higher stream reaches (e.g., headcutting). This erosion has caused substantial changes to the system, including channel widening and deepening, general loss of downstream riffle habitats, and the creation of new riffle habitats in more upstream locations. We address the impact of the rapid and ongoing geomorphic changes on Etheostoma rubrum [bayou darter; a federally listed species (Threatened) endemic to Bayou Pierre] and associated, riffle-inhabiting species, including Etheostoma lynceum (brighteye darter), Noturus hildebrandi (least madtom), Cyprinella camura (bluntface shiner), and Etheostoma whipplei (redfin darter). We first characterize stream reaches based on geologic and geomorphic data and then estimate population densities of riffle-inhabiting fishes in each geomorphically homogeneous stream reach. To assess trends in relative abundances of all riffle-inhabiting fishes and population sizes of numerically dominant riffle-inhabiting fishes, we compare relative abundances and densities from 1993–1994 with those from 1986–1988. There is an overall trend for recent erosion to occur in the upper reaches of the Bayou Pierre system, with lower reaches characterized by later, recovery, stages. Between 1940 and 1994, the point of active headcutting moved over 7 km upstream at rates of 48–750 m/yr. The relative abundances of E. rubrum and associated riffle-inhabiting fishes have not changed significantly from 1986–1994. Combined densities of all riffle-inhabiting fishes, as well as densities of three of the four most abundant species (E. rubrum, E. lynceum, N. hildebrandi), have also remained temporally stable. Overall, densities of riffle-inhabiting fishes averaged 6.7 ± 0.2/m². The density of all riffle-inhabiting fishes varied across geomorphic stages, as did the densities of E. rubrum, E. lynceum, and N. hildebrandi, with higher fish numbers in areas of active or recent erosion. This has resulted in a general pattern of greater fish densities in more upstream areas. Ultimate factors responsible for the rapid headcutting are located downstream of currently affected reaches in Bayou Pierre and the Mississippi River. These potentially include natural meander cut-offs, channel avulsion, channelization, and instream gravel mining. Thus, river-management decisions impacting areas spatially distant from the study area appear to have resulted in major local changes.