Beta diversity may be determined by dispersal limitation, environment, and phylogeographic history. Our objective was to advance the understanding of plant species turnover in rain forests in northern South America and determine which factors are affecting species beta diversity. We evaluated the relative effect of environmental variables (i.e., soil, climate, fragmentation, and flooding frequency) and dispersal limitation (i.e., geographical distance and resistance distance due mountain barriers) on tree beta diversity in 32 1-ha lowland forest plots. We found that tree species turnover was better explained by environmental distance than by geographical distance. Although soil conditions and flooding regime were good predictors of tree species composition, almost half of the variance remained unexplained. In our study system, the eastern Andean ridge had no significant effect on plant beta diversity, probably because of its young age in relation to the phylogeny. Our results provide support for the importance of environmental factors and suggest a more restricted role of dispersal limitation. Therefore, we advise that conservation strategies of lowland trees should consider specific forest types (e.g., seasonally flooded vs. terra firme, as well as piedmont vs. central Amazonian forests).