Adjacent floodplain and upland tropical forests experience the same temperature and precipitation regimes, but differ substantially in plant species composition and biotic interactions because of extensive flooding. We hypothesize that flooded forests filter fruiting traits linked to seed dispersal by water and fishes, such that selection by water and fish led to (1) trees that synchronize the timing of fruiting with annual floods, and (2) the evolution of fleshy tissues on fruits to improve buoyancy and increase fruit consumption rates by fish. To test this hypothesis, we compared plant communities in seasonally flooded forests and adjacent upland forest in terms of fruiting phenology, the frequency of trees bearing fleshy-fruit, and the role of fleshy tissues in buoyancy and seed viability. Beta-diversity in this system is high, with significant differences in species composition across habitats. As predicted, the production of ripe fleshy fruits was significantly greater in flooded than upland forests during the flood season. Furthermore, we found that trees with fleshy fruit were significantly more abundant in flooded forests even though species richness of fleshy-fruit bearing trees was proportionally similar in flooded and upland forests. Additionally, fleshy pulp increased buoyancy. Likewise, time afloat decreased for denser fruit and those with high seed to pulp ratios. In concert, these results suggest that fleshy fruits in Neotropical floodplain forests facilitated hydrochory and ichthyochory. Once established, water and fish became important agents of selection on fruiting traits.