Optimizing connectivity within and between high quality habitat patches can increase gene flow and augment available habitat for individual populations. Yet identifying and prioritizing sites for restoration and management activities is a time-consuming task that is often specific to a particular species (e.g., sport fish, species of conservation concern) and may be limited to a relatively small geographical area. Previous efforts in Missouri identified how landscape and environmental change influence fish species presence or absence, with less focus on connecting high quality habitats to one another. Our objective was to develop a flexible framework to help prioritize sites for restoration and management activities to enhance connectivity within and between aquatic communities. Using the Missouri Department of Conservation’s priority geographies and watersheds as focal areas, we employed updated habitat suitability models and network analyses to calculate metrics of connectivity weighted by habitat quality. This model can be applied to nearly any species or community across fairly complex stream networks, making this approach fairly customizable to managers focused on enhancing regional habitat connectivity. We will engage with our partners at Missouri Department of Conservation to identify additional landscape features of particular interest to managers when prioritizing sites for management actions that maximize connectivity.