This study provides regional-scale data on drivers of horseshoe crab (Limulus polyphemus) presence along the northcentral Gulf of Mexico coast and has implications for understanding habitat suitability for sparse horseshoe crab populations of conservation concern worldwide. To collect baseline data on the relationship between environmental factors and presence of horseshoe crabs, we surveyed four sites from the Fort Morgan peninsula of Mobile Bay, Alabama (AL) to Horn Island, Mississippi (MS). We documented number, size and sex of live animals, molts, and carcasses as metrics of horseshoe crab presence and demographics for two years. Data were compared to in situ and remotely sensed environmental attributes to assess environmental drivers of occurrence during the time of study. Overall, greater evidence of horseshoe crab presence was found at western sites (Petit Bois and Horn Islands) compared to eastern sites (Dauphin Island, Fort Morgan peninsula), mediated by a combination of distance from areas of high freshwater discharge and interannual variation in weather. Higher sex ratios also were found associated with higher occurrence, west of Mobile Bay. Land cover, particularly Bare Land and Estuarine Emergent Wetland classes that are common to western sites, was most predictive of live animal and to some extent carcass occurrence. Our findings suggest that small-scale variation in habitat quality can affect occurrence of horseshoe crabs in sparse populations where density is not a limiting factor. Data from molts and carcasses were informative to supplement live animal data and may be useful to enhance ecological assessment and support conservation and management in regions with sparse populations.