Habitat destruction alters the structure and spatial arrangement of remnants and creates a novel matrix, affecting the structure of biological communities. This study evaluated the contribution of patch, class and landscape level attributes of 42 wetland fragments and surrounding landscapes on the richness, abundance and presence of waterbird species. Twelve monthly censuses identified 55 species--ranging from 3 to 40 among fragments, and a total of 84,286 birds--ranging from 15 to 19,322. Wetland areas varied from 0.2 ha to 145.2 ha. The presence of 37 out of 42 species could be predicted from the structure of the fragments and the landscapes. The most important predictors were the wetland area (22 models), the rice field matrix permeability (13 models), the microhabitat richness (7 models), the wetland connectivity (5 models), and the wetland isolation (5 models). Discriminant analysis showed that fragments richer in species than expected from their areas, are found in landscapes with greater connectivity and matrix permeability than the species-poor fragments. The total area of rice fields was not related to the richness, abundance or presence of waterbirds in the wetlands fragments. The results suggest that the maintenance of the connectivity among fragments and the matrix permeability through rice-fields could be managed to foster the waterbird conservation at the landscape scale.