In turtles, the selection of the nesting area is critical for the survival of the embryos. This study investigated the environmental characteristics of nesting areas selected by Podocnemis unifilis and the spatial distribution of the nests, as well as the influence of these factors on hatching success in a floodplain area of the lower Amazon River in Brazil. The influences of the nesting date, depth of the nest, height above the river level, distance to the river and to vegetation, grain size of the substrate, and beach slope on hatching success were evaluated. Nests and randomly selected points were compared to determine if the nest sites differed from other locations on the beach, and if the females exercised control over this choice. We observed that females selected the higher sites, far from the river and next to vegetation for nesting. The nests were distributed along the beach and in the steeper “cut bank” along the outer side of bends. The main causes for loss of nests were flooding, predation and human collecting. The height of the nest above the river affected the probability of nest flooding when the river began to rise. Predation and collecting affected mainly the first nests of the season, and the collected nests also were closer to the river and vegetation, and sited higher on the beach. Keeping the nests in their natural environment is the most appropriate conservation strategy, which can be combined with protection by the local residents.