Hydrological dynamics of the Pantanal wetland drive the availability of resources and niche for aquatic and terrestrial fauna. We consider that changes in the hydrological regime of this floodplain can affect species richness, abundance and functional structure of waterbirds, wetland birds and non-wetland birds. Our study aimed to assess whether the degree of wetland dependence influences the response of bird groups to the flood pulse. We conducted the bird survey in the Paraguay River floodplain system, in five sampling sites, covering the periods of drought, flooding, full flood and ebb of the 2017–2018 hydrological cycle. Species richness and abundance were higher for non-wetland birds than waterbirds and wetland birds. On the other hand, we found that the higher the degree of wetland dependence by birds, the higher the differences in the functional-trait values. Species richness, abundance and all metrics of functional diversity varied significantly when there was an interaction between the degree of wetland dependence and the hydrological period. In all hydrological periods, bird groups occupied distinct niches. Traits such as foraging around or below the water surface were among the dominant functional traits in all hydrological periods. We emphasize the need to consider the functional traits of species in ecological studies of wetlands since measuring only species richness may not reflect the characteristics inherent to this type of ecosystem. In addition, the conservation of wetlands directly implies the maintenance of various niches throughout the hydrological periods, either for dependent or non-dependent bird species in wetlands.