In this pilot study, we evaluated the usefulness of the alkaline comet assay as a biomonitoring tool at the level of plankton communities affected by varying water quality. Zooplankton was collected in autumn 2007 and spring 2008 in two shallow lakes, one being predominantly polluted with aluminium compounds as result of water treatment process (Lake Njivice; 45°10′ N, 14°30′ E) and the other unpolluted (Lake Ponikve; 45°05′ N, 14°30′ E) used as control. Water and sediment chemistry parameters were assessed at both lake sampling sites. The results indicated that the main pollutant in both matrices was aluminium, whose concentrations exceeded the value of 0.15 mg/L −1 legally accepted for drinking water by Croatian water quality regulations. Plankton composition of the investigated lakes showed that only a few species are dominant and appear at both sites. Cladocerans are represented by Daphnia magna Straus 1820, and copepods by the calanoid Eudiaptomus padanus etruscus (Losito 1901), the cyclopoid Cyclops sp. and dipterans by larvae of Chaoborus flavicans (Meigen 1830). Other species were determined only occasionally and with low abundance. As observed, the comet assay had adequate sensitivity to detect the differences in levels of DNA damage among the dominant zooplankton taxa. Zooplanktons collected in Lake Njivice show a lower degree of DNA integrity compared with animals from the reference lake (Lake Ponikve). Inter-species variability in DNA damage was observed, indicating different genome susceptibility to the same genotoxic pollutants present in the aquatic environment. Furthermore, in the polluted Lake Njivice, seasonal differences in the levels of DNA damage within particular species of zooplankton were also noted. Calanoida, Daphnia and Chaoborus mainly had higher values of all three comet parameters in autumn 2007 than in spring 2008. Feeding modes strongly influenced the level of DNA damage in zooplankton species studied. We assume that the mechanisms of DNA damage and genotoxicity, as Water Air Soil Pollut (