We investigated the effects of threats on breeding waterbirds in the Gediz Delta, Turkey. Breeding Bird Surveys were conducted in 2002 and 2006. The survey area comprised 305 UTM grids of 1 x 1 km(2). Populations and distributions of breeding birds were compared between 2002 and 2006 for the UTM grids under threat and without any threat using paired samples t-test, Wilcoxon signed-rank test, and GIS. Urbanization, industrialization, pollution, overgrazing, disturbance, and illegal reed cutting and burning were identified in 151 (49.5%) of 305 grids in 2002. The mean total number of breeding birds per UTM grid slightly decreased in areas under threat, but significantly increased (P < 0.05) in areas without threat. The mean total number of breeding waterbirds significantly decreased (P < 0.05) in both the grids under and without threat. Out of 30 waterbirds breeding in grids under threat, 23 shifted their breeding locations. The total number of breeding pairs of 9 waterbirds decreased, 7 species increased, and 6 species were stable. The maximum breeding code of 6, maximum number of breeding pairs of 11, total number of observed birds of 11, and frequency of occurrence of 15 species significantly decreased in UTM grids under threat. Threats have significantly affected (P < 0.05) the breeding populations of bird species even in a short period of 4 years.