The rainfall regime of the Pampas region of Argentina shows a long-term cyclic behavior that has increased in intensity over the historical mean during the last four decades. In this paper we explored the effects of changes in monthly cumulative rainfall on lagoon and riparian habitat, and, in turn on the wetland waterbird community. We also explored the responses of waterbird morphofunctional groups to fluctuation in water level and habitat diversity caused by the change in rainfall at the Mar Chiquita Coastal Lagoon, Argentina (37°32’ to 37°45’S, 57°19’ to 57°26’W). Analysis of satellite images shows that increases in rainfall increased wetland water surface, but reduced riparian habitat area and habitat diversity. Increases in water surface negatively affected the abundances and species richness of waterbirds; habitat diversity did not explain a significant portion of total waterbird variability. Shorebirds (i.e., yellowlegs, plover, sandpiper) were the most affected by reduction in mudflats and habitat diversity. Other waterbirds (i.e., long-legged wading birds, waterfowls) were affected by increases in water surface (ducks, swans, long-legged waterbirds and gulls), decrease in mudflat availability (long-legged waterbirds and gulls), and decrease in habitat diversity (ducks). Our results show that the inter-annual variability in the rainfall pattern influenced the presence and abundance of most waterbirds, and species richness and composition. Fluctuation in water depth per se is known to be a key factor for habitat use of many waterbirds, but habitat diversity also needs to be considered.