Regulated rivers provide opportunities to improve habitat quality by managing the times, locations, and magnitudes of reservoir releases and diversions across the watershed. To identify these opportunities, managers select priority species and determine when, where, and how to allocate water between competing human and environmental users in the basin. Systems models have been used to recommend allocation of water between species. However, many models consider speciesβ water needs as constraints on instream flow that is managed to maximize human beneficial uses. Many models also incorporate uncertainty in the system and report an overwhelmingly large number of management alternatives. This dissertation presents three new novel models to recommend the allocation of water and money to improve habitat quality. The new models also facilitate communicating model results to managers and to the public. First, a new measurable and observable habitat metric quantifies habitat area and quality for priority aquatic, floodplain, and wetland habitat species. The metric is embedded in a systems model as an ecological objective to maximize. The systems model helps managers to identify times and locations at which to apply scarce water to most improve habitat area and quality for multiple competing species. Second, a cluster analysis approach is introduced to reduce large dimensional uncertainty problems in habitat models and focus management efforts on the important parameters to measure and monitor more carefully. The approach includes manager preferences in the search for clusters. It identifies a few, easy-to-interpret management options from a large multivariate space of possible alternatives. Third, an open-access web tool helps water resources modelers display model outputs on an interactive web map. The tool allows modelers to construct node-link networks on a web map and facilitates sharing and visualizing spatial and temporal model outputs. The dissertation applies all three studies to the Lower Bear River, Utah, to guide ongoing habitat conservation efforts, recommend water allocation strategies, and provide important insights on ways to improve overall habitat quality and area
