Florida freshwater habitats provide many essential functions including flood control and nutrient sequestration. While serving as habitat for many fish and wildlife species, wetlands also contribute significantly to the outdoor recreation industry. Despite these services, aquatic habitats contin- ue to face threats, such as urban encroachment, water withdrawals, water-level stabilization, sedimentation, non-native species introduction, cultural eutrophication, and climate change. With Florida’s increasing human population, encroachment and development continues into natural areas, stress- ing aquatic habitats and the fish and wildlife that depend on healthy wetlands. This paper summarizes a GIS process for identifying publicly accessible freshwater resources and presents a multi-criteria decision analysis tool for prioritizing those resources to guide management considerations. Publicly accessible lakes, streams, and freshwater forested and non-forested wetlands were identified, mapped, and quantified based on a suite of parameters representing their socioeconomic value, fish and wildlife value, and management emphasis (i.e., the need and opportunity for habitat restoration). We used a simple additive approach rather than a weighted overlay approach because no one parameter was deemed more important than another. Results prioritized 1235 sub-watersheds, 1835 conservation areas containing forested and/or non-forested wetlands, and 324 lakes ≥20.2 ha. Freshwater re- sources identified as high priority tended to have high values for most or all parameters measuring socioeconomic values, with more variation in values for parameters measuring value to fish and wildlife and management emphasis. Prior to development of this prioritization tool, selection of aquatic resources for enhancement and restoration projects was very subjective. This prioritization provides a quantitative, science-based decision framework to reduce that subjectivity and maintain the continuity of the prioritization and selection process. Further, the tool accounts for regional variations in aquatic resources and allows effective allocation of resources to provide the greatest sociological and ecological benefits resulting from restoration, enhancement, and management activities.