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The effects of environmental pollution on three populations of the Balkan terrapin [Mauremys rivulata (Valenciennes, 1833)] from the Bozcaada, Gökçeada and Dardanos regions were evaluated. The morphological parameters of Balkan terrapins collected on each site were measured and blood samples were taken for haematological analysis and micronucleus detection. The physicochemical, microbiological and microelement analyses of the water samples from each region were conducted by standard methods. The highest red blood cell, white blood cell and mean corpuscular haemoglobin concentration values were seen in the samples from Gökçeada. The highest haemoglobin value was found in the samples originating from Bozcaada, whereas the highest haematocrit and mean corpuscular volume values were found in the animals from Dardanos. Based on the microbiological analysis of the water samples, the most polluted site was Gökçeada. The microelement contents of the water and blood samples were different at the three sites, the lowest being in the Gökçeada area. It was revealed that the percentage of red blood cell micronuclei and other nucleus abnormalities in the M. rivulata blood samples was the lowest also in the animals living in the region of Gökçeada.