Alligator holes are a key feature of Everglades marshes that provide refugia and foraging sites for a wide range of species. We investigated the spatial pattern of alligator holes in Water Conservation Area 3, a part of the central Everglades, and examined associations among alligator holes, canals, and hydrology. There were fewer alligator holes within 1000 m of canals than expected, supporting the hypothesis that Alligator mississippiensis (American Alligator) are using canals as aquatic refugia rather than creating or maintaining alligator holes in the marsh. In addition, density of holes was associated with hydrology; specifically, areas that were drier had more than twice as many alligator holes than areas that were wetter. Analyses from this study provide a baseline for evaluating changes in location and density of alligator holes in response to canal removal and hydrologic changes that will occur as part of Everglades restoration.