The West Indian manatee (Trichechus manatus) is a Vulnerable species threatened by habitat loss in the coast of north‐eastern Brazil. This study investigates how the distribution and habitat use of the West Indian manatee is influenced by resource availability in a scenario of freshwater limitation. Land‐based and boat surveys were conducted to record manatee sightings and habitat use, in a total of 206 hours of observation. Manatee abundance was significantly influenced by freshwater availability, with greater abundances occurring close to freshwater sources. Food availability and the variation in freshwater availability between seasons were also important to determine their distribution. For the 47 manatees sighted, 39 were recorded during the rainy season and eight during the dry season. Habitat use was influenced by freshwater sources and manatees spent more time (average coefficient of area use = 24.96%) in areas with greater availability of fresh water. Under conditions of freshwater limitation, manatees were more abundant and spent more time closer to fresh water than to food sources; as a result, animals' distribution varied between seasons. The results found here can help to determine conservation strategies for the region with the highest population density and genetic variability of West Indian manatees in Brazil.