The investigation of ecological processes that maintain species coexistence is important in harsh environments, as they act as strong drivers of species selection. Congeneric species are a good model to investigate the relative importance of such processes, as closely related species tend to have similar niches. We aim to find evidence for the action and relative importance of different ecological processes hypothesized to maintain species coexistence in a tropical forest subject to seasonal flooding, using the spatial structure of populations of three congeneric species. We collected data on a 1-ha plot of a Brazilian white-sand flooded tropical forest, where individuals of three Myrcia species were tagged, mapped, and measured for diameter at soil height. We also sampled seven environmental variables in the plot. We employed several spatial point pattern models to simultaneously investigate habitat filtering, interspecific competition, stochasticity, and dispersal limitation. Habitat filtering was the most important process driving the local distribution of the species, as they showed associations, albeit of different strength, to environmental variables related to flooding. We did not detect spatial patterns consistent with interspecific competition, i.e. spatial segregation and smaller size of nearby congeners. The three species do not seem to show evidence of stochasticity even though congeners were spatially independent, since they responded to differences in the environment. Last, dispersal limitation only led to spatial associations of different size classes for one of the species. Using data from congeneric species in a harsh environment as a model, we demonstrated that habitat filtering to areas subject to flooding is the most important ecological process driving the local distribution of the species studied in a white-sand forest. Even though many studies on topo-edaphic variation in tropical forests have shown that habitat filtering is an important ecological process, other processes that drive community structuring may have gone undetected.