A study was conducted to determine the effect of water withdrawals from the University of Connecticut's (Storrs) water supply wells on the fisheries habitat of the Fenton River adjacent to the well field. The study was designed to investigate the relationships between in-stream flow and selected fish habitat in the section of the Fenton River situated in the main zone of influence of the pumping field. With the aid of historical data, new data collection, and mathematical simulation modeling, the relation between the magnitude and timing of groundwater withdrawals on the stage and flow of water in the stream was derived. Fish sampling and habitat modeling were used to assess the effects of human influence on certain reaches of the Fenton River. Among the various water management scenarios studied, several are presented that would optimize water withdrawals, while minimizing adverse effects on the stream flow and in-stream habitat.