The Topeka shiner (Notropis topeka) is a small native cyprinid species that has declined throughout its range in the Central Great Plains Region of the United States. Declines of the species have been associated with numerous factors including water quality, physical habitat alteration and predation. The N. topeka occurs in the Moniteau Creek Watershed of Cooper and Moniteau Counties of Central Missouri. We studied the Moniteau Creek population of N. topeka over a 1 y period to identify the primary physical, chemical and biological factors associated with population distributions. Fish community composition, water quality data and physical habitat variables were collected at 20 sites distributed across 8 sub-watersheds. Notropis topeka were collected at 8 of the 20 locations; 3 of these sites represent a recent within-watershed range expansion. Notropis topeka were confined to upper reaches of the sub-watersheds in areas typified by relatively high gradient and coarse substrate conditions. Water quality was significantly influenced by both precipitation and locations of sub-watersheds. Although there were isolated sub-watersheds with anthropogenic water quality impacts, we did not detect any relationships between water quality conditions and N. topeka distributions. Collectively, the data indicated that the Moniteau Creek Watershed contains a relatively stable population of N. topeka associated with good water quality and habitat conditions. This study provides baseline data that can be used to identify other watersheds where rehabilitation efforts are most likely to be successful.