Abstract Cardisoma guanhumi Latreille in Latreille, Le Peletier, Serville & Guérin, 1828, the blue land crab, is a marine semi-terrestrial crab that builds burrows in different habitats along estuaries, an ecosystem severely modified and fundamental to this endangered species in Brazil. The presence of adequate habitats and physical, chemical, and biological conditions often determine the spatial distribution of populations. We aimed to characterize the most relevant environmental conditions among the main environments present in southern Bahia state, Brazil, and evaluate their influence on the spatial distributions of C. guanhumi to define which habitats are most critical for the conservation of the species. Our results showed that there is no relationship between spatial distributions and any particular habitat, but instead to the physical and other environmental parameters studied. Low-elevation areas along the river shore, shading, a supply of leaf litter, and bare sandy substrate are highlighted as priority for the conservation of C. guanhumi. These physical factors limit the distribution of juveniles, which form dense groups on river shores without significant differences between habitats. The preservation of the native forest and restinga shrubs that border rivers appear as fundamental for the conservation of the species.