Environmental changes in estuaries resulting from resource use and management actions can detrimentally affect waterbirds. This study examined the distribution and abundance of 54 waterbird species from 1992 to 2010 in six intensively used and managed estuarine waterbodies, relative to four environmental variables (salinity, turbidity, depth variability and submerged macrophyte biomass) undergoing periodic and directional changes. Multivariate analyses enabled distinctions to be made between waterbirds associated with environmental conditions characteristic of either estuaries or estuarine lakes, and revealed spatial and temporal differences in waterbird abundances between and within waterbodies. Ducks and grebes were more abundant in low salinity deeper waterbodies, while waders, cormorants and gulls were more abundant in high salinity shallow waterbodies. Higher quantity and quality of food sources attract herbivorous waterbirds to saline lakes rather than estuaries. Water depth variability influences accessibility of feeding areas, with decreased variability in water levels increasing habitat suitability for herbivores, and reduced open periods in the estuaries decreasing habitat suitability for waders. Turbidity did not significantly influence the distribution of waterbirds, whereas disturbance from human activities and vegetation of sandbanks were considered to be important factors. The estuarine lakes systems provide a mosaic of different habitat conditions, essential for maintaining a diverse waterbird community.