Livestock watering holes (i.e., dugouts) are typically constructed in floodplains, yet the influence of dugouts on native prairie fishes is unknown. Such information is necessary for the effective management of native fishes, especially species of concern such as the endangered Topeka shiner (Notropis topeka). The goal of our study was to suggest technical guidelines for constructing floodplain wetlands that are compatible with stream fish resources. Specific objectives were to: determine the flood frequencies of the connection between streams and dugouts; determine fish community characteristics in floodplain dugouts; and, associate dugout characteristics with fish assemblages. A total of 20 dugouts within Six Mile Creek watershed, South Dakota, were surveyed seasonally (excluding winter) from fall of 2003 to fall of 2004. Dugouts were categorized according to their lateral floodplain placement (connectivity with the stream and flood frequency of the stream-dugout connection) and longitudinal placement across the watershed. Fishes were sampled in dugouts and adjacent stream reaches with seines and traps. The 21 species making up the stream and dugout fish assemblages were similar. Fish inhabited 65% of the dugouts; 30% contained Topeka shiners. Most fish inhabitance, and all Topeka shiner occurrences, were in dugouts that were headwater sites and were either directly connected to the stream or disconnected and frequently flooded (average 1 in 2 year event). Two dugouts in this latter category contained the most abundant, self-sustaining Topeka shiner populations. Constructing dugouts separate from the stream within frequently inundated zones can provide off-channel habitat for fishes.