During 2009–2011 we investigated the effect of perennial and roosting cormorant (Phalacrocorax carbo sinensis) colonies on microbial pollution in 3 lakes: Góreckie (Greater Poland National Park), Chrzypsko (Greater Poland Province) and Ostrowiec (Drawa National Park). On Lake Góreckie cormorants formed a roosting colony (<200 individuals) that inhabited part of the lake shore. On Lake Chrzypsko a new breeding colony was formed (3 nests) while the breeding colony on Lake Ostrowiec, established over 40 years ago, consisted of over 170 breeding pairs. In the case of Lake Ostrowiec, high pollution with coliform bacteria (including Escherichia coli) was observed. Compared to the control station the significantly higher Most Probable Number (MPN) of coliform bacteria was found in groundwater under the colony. It was found that bacterial counts decreased in the direction of the centre of the water body with the highest numbers noted in the lake samples collected within the colony boundaries. Furthermore, seasonal variations in coliform bacteria were also observed with maximum densities during the breeding season. Similar trends were observed for the roosting colony on Lake Góreckie while for the newly forming colony on Lake Chrzypsko increased density of investigated bacteria was noted only in groundwater.