Anuran distribution patterns can be influenced by structural and dynamic characteristics of a habitat. In floodplains—such as the South American Pantanal wetlands—cyclic changes within terrestrial and aquatic biotopes can limit the distribution and occurrence of species. To test the influence of the habitat on the anuran community structure in the Pantanal, we recorded data on species composition and abundance at 30 sampling plots, from October 2006 to May 2007. We also recorded data on seven local environmental variables: water depth, distance to the nearest permanent water body, hydroperiod, leaf litter volume, plant cover by herbaceous plants, by monospecific stands of a bromeliad, and by shrubby/arboreal woody plants. We used multivariate statistical analyses to test for data correlation. In addition, we analyzed the degrees of associations of anuran species to habitat types. Our results revealed no influence of any of the analyzed environmental variables on the anuran species richness and abundance. However, species composition varied with vegetation structural complexity and the hydroperiod. Although most anurans were able to occupy different habitats along the environmental gradient, six species were strongly associated with specific habitats. The homogenizing effect imposed by floods on different habitat types might overshadow distributional patterns resulting from species-specific attributes, as well as from influences of other environmental factors.