Drinking water producers have a far-reaching responsibility to provide safe, clean and wholesome drinking water, using water resources possibly effected by the thousands of chemicals used in societies’ daily life. This study has monitored chemical hazards in drinking water from source to tap, using effect-based methods. The study was conducted at a Swedish drinking water treatment plant sourcing lake water and aimed to investigate potential seasonal variations in both the raw water and water after different treatment steps. Furthermore, a granular activated carbon (GAC) pilot facility was evaluated. Samples were analyzed for estrogenicity, androgenicity, aryl hydrocarbon receptor (AhR) activity, oxidative stress (Nrf2) response and genotoxicity (micronucleus formation). We observed seasonal differences in oxidative stress and genotoxic effects in both raw and drinking water with higher activities during the late fall of each year. The removal efficiency for both oxidative stress and genotoxicity was limited in the full-scale treatment process and occasionally the genotoxicity was also detected in outgoing drinking water from the treatment plant and in samples collected at consumers tap on the distribution network. AhR activity was present in all raw water samples and the removal was limited. Estrogenic activities were observed in most of the raw water samples but in contrast to the other parameters estrogenicity was effectively reduced by the full-scale conventional treatment. The GAC pilot treatment was generally more efficient than the full-scale conventional treatment in removing all observed bioactivities and could be a viable complement to the current treatment to assure drinking water free from genotoxic compounds. Genotoxic activities in drinking water was observed while all currently regulated chemical parameters were fulfilled. This highlights the need for effect-based monitoring in efforts to ensure the chemical safety of drinking water, as target chemical analysis of single compounds will overlook both unknown hazardous compounds as well as potential mixture effects.