Water quality in the Karašica drainage channel in Baranja is under a strong influence of anthropogenic sources (agriculture and municipal wastewaters), and the input of polluted waters into this watercourse also depends on seasonal changes in climate parameters. Significant changes in specific conductivity before and after the discharge site were indications of wastewater inflow. High concentrations of enterococci and E. coli were good indicators of recent faecal contamination with wastewaters, while the presence of specific pollutants (organochlorine pesticides, hexachlorocyclohexanes, and DDT and its metabolites), as well as metals, evidently derived from agricultural run-off, especially in the autumn. Selected parameters in the Lemna-test (growth rate and yield, photosynthetic pigments, total soluble proteins and malondialdehyde) proved to be useful indicators of the influence of present pollutants in the investigated waters on L. minor. Low levels of nutrients in the water, especially nitrogen and high levels of specific contaminants, have caused growth inhibition of L. minor associated with enhanced lipid peroxidation, as well as decreased Chla/b and Chl(a+b)/Car and reduced protein concentrations in almost all water samples of the drainage channel. A more accurate assessment of water quality was achieved by using Lemna test with relevant structural or functional endpoints (morphological changes, pigments, proteins and lipid peroxidation) and by considering time-varying exposure of different sources of pollution.