This project provides a better understanding how linkages among surface-water availability, connectivity, and temperature mediate habitat and trophic dynamics of the Fish Creek Watershed (FCW). These interrelated processes form a shifting mosaic of freshwater habitats across the landscape that can be classified, mapped, understood, and modeled in response to past and future climate and land-use change in a spatial and temporal context. Developing scenarios of freshwater habitat change in this context provides managers and scientists with a flexible template to evaluate a range of potential responses to climate and land-use change. Applying this approach in the FCW is made feasible because of the availability of pre-existing geospatial and monitoring datasets and is immediately relevant to management because of ongoing and planned subsistence and industrial activities. Focusing on this watershed additionally leverages ongoing studies being supported by the Bureau of Land Management, U.S. Fish and Wildlife Service, U.S. Geological Survey, University of Alaska Fairbanks, and the National Science Foundation, along with industry sponsored studies. This study used a phased approach resulting in an integrated landscape-scale and spatially explicit model template for managers, scientists, and other stakeholders, which can be enhanced through more focused biological studies.