Anthropogenic pollution of freshwater ecosystem is an important environmental issue. Zooplankton community is one of the most sensitive components to the changes in the level of water pollution. The mobility of the structural organization of zooplankton is linked to different tolerance ranges of the species that form a community. Anthropogenic pollution can cause changes in the physico-chemical state of the aquatic environment and disturb the ecological balance of the ecosystem. A total number of 52 zooplankton samples were collected and analysed in the litoral zone of the Prut ecosystem in 8 collection stations, namely Costesti-Stinca, Braniste, Sculeni, Leuseni, Leova, Cahul, Cislita-Prut and Giurgiulesti. The water quality of the Prut river according to the indices of saprobity of the indicator species of zooplankton can be ranged in class II, which is "good quality". The level of pollution of the investigated ecosystem was characterized as a clean one. The Prut river is an oligo-mesotrophic basin with sectors of toxic effects of pollutants and eutrophication, however with a good compensatory potential for restoration and adaptation of zooplankton organisms.