As part of an effort to balance urban needs with preservation of sensitive fish habitat, CE-QUAL-W2, a hydrodynamic and temperature model, was developed for Chester Morse Lake and the lower Cedar River, WA. Cedar River model starts downstream of the Chester Morse dam and ends 21 km downstream at Landsburg, where drinking water is diverted for the City of Seattle. This water quality model was coupled with a fish habitat and bioenergetics model for bull trout and was calibrated to temperature data between 2005 and 2008. The CE-QUAL-W2 model was found to be highly accurate in modeling temperature variation in the lake - at most locations having an average absolute mean error of between 0.5 and 0.8 oC. The Cedar River model had an average absolute mean error of 0.7oC. This tool is designed to allow managers and operators to estimate the impact on fish habitat and growth potential from various management decisions including extent of drawdown, timing/volume of flows, and pumping operations. Future studies could include incorporating further water quality parameters such as nutrients, algae, and zooplankton as they relate to fish productivity.