The Topeka shiner (Notropis topeka) lives in high quality water prairie streams usually in areas with sustained permanent water. In South Dakota, the shiner inhabits the upper tributaries of the James, Vermillion, and Big Sioux rivers [Shearer, J.S., 2003]. This minnow-sized fish is endangered due to sedimentation, pesticide residues, animal waste and habitat fragmentation. Habitat and population fragmentation occur for a number of reasons including road crossings which often act as barriers to aquatic species. Ensuring habitat connectivity is critical to the sustainability, refounding and overall viability of the species’ metapopulation. Barriers such as culverts provide efficient and cost-effective methods of conducting water under roadways but may limit aquatic species movement if not correctly designed, installed and maintained. This project will investigate the effect of culverts as barriers, examining factors that prevent, limit or allow movement of Topeka shiners in these watersheds as well as the effect of culvert barriers on the fishes’ distribution and genetic diversity. The project will help identify the best culvert designs as well as culvert retrofitting and installation for road crossings to minimize the potential of future impacts on connectivity of aquatic species including the Topeka shiner.