America's waterways face multiple pressures that have the capabilities to alter the hydrologic connectivity that maintains aquatic population persistence throughout the watershed. The dynamic feedback of organism response can provide a real-time link between the habitat-influencing hydrologic processes operating within a watershed and the ecological processes that shape aquatic communities. This paper describes the incorporation of a connectivity component into the habitat-selection behavior of fish during high-flow conditions. The research is part of a larger effort that focuses on the development and use of a spatially-explicit individual-based model (IBM) in evaluating the long-term hydrologic effect of landscape change and management on aquatic communities. The model simulates the behavior of individual fish in their habitat selection process to analyze network dynamics in stream ecosystems in response to outside driving influences. The primary input to this model is streamflow and hydrologic connectivity related to watershed landscape characteristics. The results of this research show that connectivity does in fact contribute to the ability of aquatic communities to tolerate and recover from high-stress conditions. However, despite the recognition of the importance of connectivity in watershed science, it has not been directly incorporated into models of large-scale riverine systems. This work shows that connectivity, in addition to habitat quality, can influence species distribution within river reaches and affect population sustainability throughout the watershed area.