The importance of subaquatic structures in determining fish assemblages is well documented in the literature, but few studies have examined the influence of submerged vegetation resulting from river impoundments in which arboreal vegetation was not removed. The purpose of this study was to evaluate the role of submerged trunks determining abundance and composition of fish assemblages by comparing habitats with and without them in two reservoirs of different ages. The results of this study demonstrated the importance of structured areas (with submerged vegetation) to the abundance of fish in both reservoirs. However, the role of these structures in maintaining species richness and diversity was significant only during the initial years after the impoundment. The occupation of these habitats by small invertivorous fish indicates that the nonremoval of arboreal vegetation in these reservoirs contributes to the increase of their biogenic capacity. In addition, vegetation provides shelter against predation. Considering the conservation of fishery resources, we conclude that the pre-removal of arboreal vegetation in new reservoirs should be allowed only to the extent necessary to maintain acceptable water quality, even considering transitory and localized hypoxic processes.