While all sirenian species are considered sentinel animals for the ecological health of their habitat, they are currently facing extinction risk. The Antillean manatee (Trichechus manatus manatus) is classified as an endangered species in Brazil. Its distribution and behaviour are mainly influenced by the presence of aquatic vegetation, freshwater and anthropogenic activities, as well as by variations in tides, temperature and salinity. The study investigated the behaviour of manatees in the Barra do Rio Mamanguape Environmental Protection Area in north‐eastern Brazil, and the relationship between these behaviours and the biotic and abiotic characteristics of this estuarine environment. The behavioural data were collected between November 2016 and May 2017, during 35 days of monitoring. The records of surface behaviour were obtained using animal focal sampling. Anthropogenic activities were recorded qualitatively and quantitatively during the surveys. Warmer water (30–31°C), reduced turbidity (1–2 m) and sandy sediments had a significant influence on the behaviour of the manatees. The manatees presented neutral behaviour more often than expected in response to anthropogenic activities, which indicates that the animals were undisturbed by these activities. This is the first systematic study of the influence of biotic and abiotic factors on the behaviour and ecology of Antillean manatees in a protected area of a tropical region, providing important new insights into the behavioural ecology of an endangered species. The Barra do Rio Mamanguape Environmental Protection Area seems to fulfil the goal of adequate management and conservation of manatees in a tropical region. Specifically, it shows that appropriate management, law enforcement and inspection measures are essential for maintaining endangered populations.