Marine and estuarine habitats of Florida are biologically productive and economically valuable. They provide a diversity of species with spawning grounds, nurseries, shelter, and food, augmenting fisheries production and supporting a vibrant natural resources-based economy. Additionally, these habitats shelter coastal areas from storm damage, maintain water quality, produce oxygen, and sequester carbon. Although substantial conservation efforts have been implemented to conserve estuarine and marine habitats, these resources continue to be threatened by shoreline development, altered hydrology, pollution, dredging, mosquito-control impoundments, and climate change. Because of rapid human population expansion, economic growth, and related development pressures, Florida faces the challenge of balancing human requirements with those of natural resource conservation. To inform conservation of these resources, a geographic-information-system-based process was used to develop a multi-criteria decision analysis tool and prioritize those resources for actions related to habitat restoration and enhancement. Estuarine and marine habitats were identified, mapped, and quantified based on a suite of parameters representing their socioeconomic, fish, and wildlife values, and the need, feasibility, and potential for habitat restoration. A total of 283 sub-watersheds (National Hydrology Dataset HUC 12) containing 1,061,864 ha of estuarine habitat and 9244 5-km2 gridded cells of marine habitat were prioritized for conservation. This prioritization process provided scientifically based regional and statewide maps directing conservation efforts for estuarine and marine habitat into the foreseeable future. The spatial products from this evaluation can be combined with those for freshwater habitats in Florida to allow for landscape-scale management of aquatic resources across ecosystems while sequencing and connecting upstream and downstream projects to achieve optimal desired outcomes.