The aim of this study was to present the first detailed analysis of long-term population estimates and trends of waterbirds wintering at Messolonghi lagoons, one of the largest Greek wetlands, during 1982 to 2012, using TrendSpotter software. The wetland supported on average 63,054 ± 22,241 (SD) birds (range 29,630 to 109,795), with waterfowl and their allies being the most abundant group, by both species and numbers. Over 70% of the 28 most abundant species (19 waterfowl, 9 waders) were increasing (14 waterfowl, 6 waders), 4 waterfowl were decreasing, 3 species remained stable (1 waterfowl, 2 waders) and 1 wader could not be assessed. In total, waterfowl increased by 2%, waders increased by 4% and the overall species assemblage increased by 2.2% over the 31-year period. The wetland is of international importance for waterbirds in general and for Eurasian wigeon Anas penelope and Kentish plover Charadrius alexandrinus specifically. In addition, 7 other species (6 waterfowl, 1 wader) currently exceed the 1% flyway population threshold and could also be considered as of international importance in the future. Long-term increases in the numbers of most waterbirds were detected, and internationally important populations were identified, thus highlighting Messolonghi lagoons' increasing significance for wintering waterbirds over the past 31 years. Piscivores (i.e. pelicans, cormorants, herons and egrets), flamingos and small waders showed the strongest increases in numbers. In contrast, common pochard Aythya ferina and tufted duck Aythya fuligula showed the greatest declines. In most species, population trends followed those occurring at the flyway level, suggesting that regional or international rather than local factors may be mainly responsible.