Use of rice fields as complementary habitats to waterbird species was investigated. Three questions were posed (1) does waterbird richness (defined as number of species), abundance and composition differ between rice fields and natural wetlands; (2) do richness, abundance and composition of waterbird species differ between flooded and drained rice fields in the post-harvest season, and (3) do richness, abundance and composition of waterbird species change in rice fields over the rice cultivation cycle? Eight collections were made in eight rice fields with different hydrological conditions after cultivation (four dry and four flooded) and four natural wetlands. Waterbirds were censused using binoculars and one telescope. A total of 76 waterbird species were observed during the study period (2005–2006): 59 species in rice fields and 70 species in natural wetlands. The richness of waterbirds was higher in natural wetlands than flooded and drained rice fields; however, there was no difference between flooded and drained rice fields. The richness of waterbirds did not change over the rice cultivation cycle. Waterbird abundance was higher in natural wetlands than in flooded and drained rice fields. Natural wetlands showed a seasonal pattern of species composition and abundance different from rice fields. Rice fields are used for an important fraction of the waterbird richness in southern Brazil, acting as habitat complementary for biodiversity, but in lower richness and abundance when compared to natural wetlands. The non-intentional flooding of rice fields did not contribute towards waterbird conservation in southern Brazil.