The Cichlidae are among the most diversified families of fish in the Neotropics and represent an important component of aquatic biodiversity. Understanding cichlid nest‐site selection is important for assemblages facing uncertain futures due to species invasions and environmental change. This information could be used to predict how inter‐ and intraspecific competition for reproductive space may affect populations with changing community dynamics or to identify areas as targets for conservation. We investigated which hydrogeomorphological factors correlated to preferred nest sites of four native cichlid species in the Bladen River, Belize. We recorded the locations of nest sites and collected habitat data through the study reach, including flow velocity, depth, sediment type, fish cover type richness and distance to the bank. Nest locations and physical habitat data were used to construct spatially explicit habitat models using boosted regression trees (BRTs). The models provided statistically significant evidence that physical habitat variables influence the distribution of the nest sites. We found that all species except Archocentrus spilurus were associated with substrate, specifically sand. Thorichthys meeki was also associated with lower water velocities, whereas Cichlasoma salvini was influenced by all five variables. Vieja maculicauda and Archocentrus spilurus were both influenced by flow velocity, distance to bank and depth, although A. spilurus preferred deeper, slightly faster locations about the same distance to the bank. This study suggests that the spatial distribution of nest sites within this cichlid community is significantly different than random and is at least partially governed by physical controls.