In many lowland floodplains around the world, upriver interferences to flows (weirs, dams, off-takes) have led to much reduced frequency and duration of flooding. As a result, many floodplain wetlands are now inundated relatively rarely if at all. Given regulation of most lowland rivers in southeastern Australia, we assessed use of wetlands by birds in the essentially unregulated Ovens River in northeastern Victoria. Twelve sites (0.4–1.2 ha) were studied after flooding. Four sites were ‘permanent billabongs’, four were temporary wetlands and the other four were randomly selected woodland sites >60 m from the nearest water body (including the river) acting as ‘control’ or ‘reference’ sites. Aquatic birds were not recorded using woodland sites, but many species were differentially associated with either billabongs or temporary wetlands. A surprising number of non-aquatic birds either exclusively or differentially were associated with wetland sites compared with woodland sites. We concluded that heterogeneous macrohabitat will increase local avian biodiversity on lowland floodplains. Moreover, densities and diversity of non-aquatic, woodland species also increased with the presence of wetlands. Temporary wetlands were used differently from permanent billabongs by birds, especially in foraging methods. This suggests that the reinstatement of major flooding on heavily regulated floodplains would be ecologically advantageous for birds by providing foraging and breeding opportunities.