Freshwater habitats are among the most impacted ecosystem on Earth. Consequently, reserves have been implemented in an attempt to reduce the threat to freshwater biodiversity. However, few studies have evaluated how effective these protected areas (PA) are for the conservation of freshwater organisms. In the present study, we compared species richness, community composition and density of small-bodied fishes between lagoons within an eight-year-old reserve (i.e. protected lagoons) with those outside the reserve (i.e. unprotected lagoons) in a river-floodplain system that is exposed to seasonal flooding. The unprotected lagoons have been submitted to a light fishing pressure mainly targeting small-sized fishes for sale as baits. Our results showed no differences between the lagoons inside the reserve with those outside in any of the community properties measured. However, we registered an overall tendency of abundance reduction among the species used as baits in unprotected lagoons. Considering the high degree of oversight in the PA and the low fishing pressure among unprotected lagoons, it is possible that the positive effects promoted by the reserve on fish assemblages are being exported towards unprotected lagoons and thus offsetting a portion of the anthropogenic impacts. We conclude that the protection provided by the reserve is very efficient in river-floodplain systems, because not only it protects the biota inside the reserve but also act as a source of propagules to unprotected areas during the rainy season when all the aquatic subsystems are connected by the flood.