Juvenile sport fish such as common snook (Centropomus undecimalis) and tarpon (Megalops atlanticus) rely on nursery habitats that are isolated from large predatory fish, such as coastal ponds in southwest Florida that have limited connectivity to the estuary. However, changes in the hydrology surrounding these ponds driven by increased development, stormwater infrastructure construction, and sea level rise may alter the habitat features that make them desirable to these species. As part of a collaborative, multi-agency project supported by the NOAA RESTORE Science Program, a Habitat Evolution Model is being used to predict potential hydrologic changes around these habitats under various sea level rise scenarios. A GIS-based marsh evolution model calibrated for tropical habitats was used to predict the location of future vegetation cover classes and quantify changes at defined time steps. Two-dimensional HEC-RAS modeling was applied to predict changes in coastal pond flooding frequency, a factor influencing nursery habitat quality for juvenile sport fish. The outputs of these models will be incorporated into a Habitat Assessment and a Conservation Opportunities Index designed to help local government prioritize the conservation of ponds projected to be most vulnerable to future impacts and the most valuable to juvenile sport fish. Additionally, restoration practitioners can apply lessons learned from two nearby successful sport fish nursery restoration projects—Lemon Creek Wildflower Preserve in Charlotte County and Robinson Preserve in Manatee County—to better focus their limited resources on the enhancement or creation of desirable habitats.