We surveyed broad-snouted caiman Caiman latirostris, marsh deer Blastocerus dichotomus and capybara Hydrochaeris hydrochaeris along the Paraná River of southeastern Brazil in the area to be flooded by the Porto Primavera Dam. We conducted night-light counts along 124 km of the Paraná River and its tributaries. The mean observed density was 0·12 caiman per km surveyed. We counted caiman nests, marsh deer, and capybara groups over 957 km 2 of habitat representing 43% of the area to be flooded, by means of aerial survey. The mean estimated density was 0·49 caiman nest/km 2, 0·51 deer/km 2, and 0·16 capybara groups/km 2. Extending these results to the 1280 km 2 of floodplains in the area, we estimated 630 caiman nests per year, 650 marsh deer, and 200 groups of capybara to occur in the area. We recommend the creation of a protected area to guarantee the survival of the broad-snouted caiman and marsh deer in this region.