Despite remarkable significance of Pantanal for the conservation of aquatic birds, the status of their populations, the spatiotemporal patterns of distribution and habitat use and structure of communities are little known. Thus, we studied three aquatic environments (Negro river, bays and salines) from 2007 to 2009 in the Nhecolândia Pantanal to verify the distribution and composition of aquatic birds and also if there is significant seasonal influence on these aspects. We adopted the transect method (288 hours of sampling) and recorded 135 species (7.834 individuals). The Negro river showed the highest diversity, while the salines the lowest. The similarity of aquatic bird communities was higher between bays and salines, followed by Negro river and bays and lower between salines and Negro river. The equidistribution is more variable in the salines and more stable in the Negro river. The environments strongly differ from each other in aquatic bird composition in space (habitat use and distribution) and time (seasonal water fluctuations). The diversity of bird community in the dry season varies significantly in the salines, followed by the bays and more stable in the Negro river. The Negro river, regardless of large annual amplitude of flow, is more seasonally stable since its riparian vegetation is continuous (not isolated) and constant. These aspects provide better conditions to stay all year, contributing to decrease the seasonal nomadic tendencies of aquatic birds. Finally, all these data provide strong arguments to the preservation of all phytophysiognomies in the Nhecolândia sub- region of Pantanal, but with special attention to the salines widely used by many flocks of aquatic birds (mainly in the dry season) and migrant and/or rare species restricted to this habitat.