In seasonally flooded wetlands, natural disturbances such as flooding and associated organic debris deposition followed by a drawdown period provide various opportunities for plant species regeneration, which can promote plant community diversity across space and time. Specifically, regeneration may be influenced by the direct effect of flooding on seed dispersal and seedling emergence as well as the indirect effect of organic debris on seed trapping and germination. Our objective was to examine the influence of seasonal flooding, topography, and cover of organic debris on seedling distribution in seasonally flooded grassland of the Pantanal. We measured species richness and abundance of seedlings for three years at three topographic levels with variable coverage of organic debris at the end of the flood season, and during the dry season when there was no debris deposition. A total of 43 species were recorded with no difference in species richness between immediate post-flood and dry seasons. However, the abundance of some species was higher post-flood than during the dry period. The distribution of seedlings differed between topographic levels post-flood with the greatest seedling abundance and richness occurring at the medium level, followed by the high and finally the low level, this was due to the higher concentration of organic debris in the low-level. Our results indicate that areas with predictable annual floods promote the individual species adaptation for successful regeneration.