Habitat cover and change were analysed in the Marmara Lake to investigate the effects of water level and human intervention on the natural habitats and breeding waterbirds. Breeding Birds Surveys were applied to investigate breeding waterbirds and their breeding activities in 2008 and 2011. GIS, remote sensing techniques and various satellite images were used to determine distributions, surface areas, zonal centroids, and displacements of the habitats in 2000, 2008 and 2011. The total number of bird species with and without breeding evidence in 2008 and 2011 were compared with the Chi-Square test. Habitats in each UTM grid in 2008 and 2011 were compared with McNemar's test. The impact of water level on habitats, number of breeding birds, and their breeding parameters were investigated using Spearman's correlation analyses.