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Humans have substantially altered the thermal regimes of freshwater habitats worldwide, with significant environmental consequences. There is a critical need for a comprehensive modeling framework for forecasting the downstream impacts of two of the most common anthropogenic structures that alter river water temperatures: 1) dams that selectively release water from thermally stratified reservoirs, and 2) power generating stations and industrial plants that use river water for once-through cooling. These facilities change the thermal dynamics of the downstream waters through a complex interaction of water release volume and temperature and the subsequent exchange with the environment downstream. In order to stay within the downstream temperature limits imposed by regulatory agencies, managers must monitor not just release volumes and temperatures, but also need to be able to forecast the thermal impacts of their day-to-day operations on habitat which may be hundreds of kilometers downstream. Here we describe a coupled modeling framework that links mesoscale weather and ecological models to generate inputs for a physically-based water temperature model for monitoring and forecasting river temperatures downstream from these facilities at fine spatiotemporal scales. We provide an example of how this modeling framework is being applied to a water allocation decision support system (DSS) for the management of Endangered Species Act (ESA) listed salmon species in the Sacramento River in California.