Kalametiya Lagoon, a highly threatened Sri Lankan wetland, has undergone drastic hydrological changes in recent decades, due to an upstream irrigation project. These changes led to the invasion of the lagoon water by monospecific Sonneratia caseolaris mangrove stands and Typha angustifolia reedbeds. As Kalametiya has been a nationally recognized bird sanctuary since 1984, this invasion is expected to have brought significant changes upon local avifauna. Therefore, this study aimed at determining the lagoon’s current bird diversity and distribution in relation with habitat types and environmental variables. Thirty-seven point-count stations were studied, between January and April 2022. Seventy-nine bird species, including four endemic and ten nationally threatened species, were encountered during the study period. Invertebrate feeders and polyphages were the richest and most diverse guilds. Bird communities were also found richer and more diverse in T. angustifolia reedbeds than in S. caseolaris mangroves. As feeding guild composition was significantly influenced by several environmental variables (i.e., water nitrate content, water TDS, water pH, soil pH), guilds could have great potential as bioindicators of the ecosystem if further studies are done to explore these relationships. Considering the important bird diversity found in the new habitats, this research brings additional proof that a management aiming at restoring the lagoon to its past state would bring significant changes to its avifaunal community. These changes could, in the future, be more precisely defined by a thorough comparison with past inventories of the lagoon’s bird community.