The structure of the waterbird community at Lago Salso in Southern Italy, Apulia, was surveyed over a 4-year period (2003–2006), during the breeding season (May-July). Lago Salso is an artificial lake with high water levels. Flooding of the surrounding fields, due to copious seasonal rainfalls, occasionally forms vast swampy wetlands around Lago Salso. The variation in waterbird structure and composition, concomitantly with the occurrence of these flooded habitats, is described. In particular, during 2003–2005 there was little variation in annual species richness and diversity at the lake. However, in 2006 the waterbird community changed in species composition and significantly increased in species richness (from 21 ± 3.8 to 32 ± 2.5 species) and abundance values (from 222 ± 167 to 988 ± 42.4 individuals) with the presence of wet grasslands. Lago Salso is one of the most Important Bird Areas on the Italian peninsula, and the occurrence of several species with high conservation value almost exclusive to wet grassland has important implications from a conservation point of view. The formations of temporary flooded meadows are rare in the south of Italy, and our results emphasize the need to define management guidelines for the maintenance of such flooded grasslands.