Temporal turnover of species between predominantly aquatic and terrestrial phases of floodplains, a process that helps maintain the high bird diversity of river–floodplain systems, could be driven by dependency of species on wetlands. To assess this, we compared the bird assemblages of river–floodplain systems at 60 sites along the Paraná River during the nonbreeding seasons of 2011, when water levels were predominantly high (high‐water year), and 2012, when levels were predominantly much lower (low‐water year). Birds were sampled by point counts repeated four times during each year at each site. We tested whether temporal patterns differed between wetland‐dependent and nonwetland‐dependent birds because these groups show positive and negative relationships, respectively, with water‐level increases. Species composition varied between years. Ten of the 14 species associated with high water levels in 2011 were waterbirds, and 11 of the 14 species associated with lower water levels (2012) were nonwetland species. Species richness and abundance per site of waterbirds and abundance of wetland species were higher during the high‐water year than in the low‐water year. Species richness, abundance, and diversity per site of nonwetland birds were, on the other hand, higher during the low‐water year than in the high‐water year. Species turnover between predominantly high‐ and low‐water periods did not respond to shorter term water‐level fluctuations within each year. In conclusion, our results show that degree of wetland dependence drives bird species turnover as a function of water‐level fluctuations, showing the importance of hydrological variability for bird conservation in river–floodplain systems.