In this study we evaluated genotoxicity and cytotoxicity of native samples of wastewaters (15 samples), surface waters (28 samples) and potable waters (8 samples) with the SOS/umuC assay with Salmonella typhimurium TA1535/pSK1002 and MTT assay with human hepatoma HepG2 cells. The genotoxicity of selected samples was confirmed with the comet assay with HepG2 cells. In the SOS/umuC assay 13 out of the 51 samples were genotoxic: two effluent samples from chemical industry; one sample of wastewater treatment plant effluent; two hospital wastewater samples; three river water samples and four lake water samples. Six samples were cytotoxic for HepG2 cells: both effluent samples of chemical industry, two wastewater treatment plant effluent samples, and two river water samples, however, only the chemical industry effluent samples were genotoxic and cytotoxic, indicating that different contaminants are responsible for genotoxic and toxic effects. Comparing genotoxicity of river and lake water samples with the chemical analytical data of the presence of the residues of pharmaceutical and personal care products (non-steroidal anti-inflammatory drugs, UV filters and disinfectants) in these samples, indicated that the presence of UV filters might be linked to the genotoxicity of these samples. The results showed that the application of the bacterial SOS/umuC assay and mammalian cell assays (MTT and comet assay) with HepG2 cells was suitably sensitive combination of assays to monitor genotoxicity and cytotoxicity of native samples of wastewaters and surface waters. With this study we also confirmed that the toxicity/genotoxicity bioassays should be an integral tool in the evaluation of toxicity of complex wastewaters before the release into environment, as well as for the monitoring of surface water quality, providing data useful in risk assessment.