Research Highlights: Seasonally flooded and terra firme forests are characteristic ecosystems of the Colombian Orinoco Basin and of great importance in the maintenance of regional biodiversity and ecosystem function. These forests have a unimodal precipitation regime that can cause a temporal effect on the seedling regeneration niche. This could partly explain the high diversity and coexistence of plant species in these forests, as well as the similarity in composition of seedlings and trees. Background and Objectives: Seedlings are a key factor in the assembly of plant communities. We evaluated the effect of flooding and rains on the dissimilarity and compositional affinity between trees and seedlings of seasonally flooded and terra firme forests. Materials and Methods: the tree community of these forests in San Martín (Meta, Colombia) was characterized and compared with their respective seedling communities before (June) and after (December) rain and flooding (during the rainy season). We evaluated plant species diversity and abundance (Shannon diversity and Pielou eveness index), as well as the compositional dissimilarities of each tree community with their corresponding seedling community sampled at the beginning and end of rains and flooding (Bray–Curtis dissimilarity). We also compared sampling site composition using a NMDS analysis. Results: We found that the terra firme forest had higher diversity compared to the flooded forest. Seedling density in the seasonally flooded forest decreased significantly after the flood but not in the terra firme forest at the end of the rainy season. The compositional dissimilarity between trees and seedlings in the seasonally inundated forest also decreased after the flood. However, this pattern was not evident in the terra firme forest. Conclusions: These results indicate that seasonal flooding generates a strong ecological filter that affects the realized niche of plants in these forests. Our results can contribute valuable information for the effective development of assisted restoration and conservation programs.