Everglades restoration will alter the hydrology of South Florida, affecting both water depth and salinity levels in the southern fringes of the Everglades, the habitat of the endangered American crocodile (Crocodylus acutus). A key question is what the effects of these hydrologic changes will be on the crocodile population. Reliable predictions of the viability of endangered species under a variety of management scenarios are of vital importance in conservation ecology. Juvenile American crocodiles are thought to be sensitive to high salinity levels, suffering reduced mass, and potentially reduced survivorship and recruitment. This could negatively impact the population recovery. We addressed the management issue of how the crocodile population will respond to alterations in hydrology with a spatially explicit individual-based model. The model is designed to relate water levels, salinities, and dominant vegetation to crocodile distribution, abundance, population growth, individual growth, survival, nesting effort, and nesting success. Our analysis shows that Everglades restoration, through its effects on water flow to estuaries, may benefit crocodile populations if increased freshwater flow reduces the chance that regional salinity levels exceed levels where small individuals lose mass. In addition, we conclude that conservation priority should be placed on reducing anthropogenic sources of mortality on large individuals, such as road mortality. Finally, research should focus on estimates of annual survivorship for large individuals.