Abstract Background Predicting how natural and anthropogenic drivers shape different ecological indicators, such as plant populations along environmental gradients, can be a relevant tool for establishing management and conservation criteria of tropical wetlands. We aimed to assess the effects of seasonal flood disturbance, type of grasslands and topographical conditions on Croton trinitatis population distribution in a tropical wetland. Methods The study was carried out in a seasonally flooded grassland (Central-West Brazil). We conducted samplings of soil on the dry and flood hydrophases of the Pantanal. We took the samples in eight seasonal ponds, with 1 km interval between them. Transects were marked during the flood period, observing the water level, one in the lowest zone, in the middle of the pond = low (ca. 60 cm deep), one at the pond edge = mid (ca. 30 cm deep) and one in the higher zone, on the external part = high (ca. 1 cm deep). Results The results showed that the topography, seasonality, and types of grassland determine differences in the abundance patterns of adult plants and seedlings, and seed bank and seed predation. The abiotic factors can shape plant population-related ecological processes and patterns, with outputs (germination and predation) and inputs (local dispersion and from neighbouring areas) of proportional seeds for the population maintenance in this environment. Conclusion We emphasize the importance of these findings, to show that abiotic factors are not the only ones to be considered in ecological studies of distribution and structuring of populations in habitats with extreme seasonal events.