Cyanotoxins can be produced in surface waters by cyanobacterial blooms, mostly during summer and early autumn. Intoxications would result from consumption of water contaminated with the potent hepatotoxins, microcystins and nodularin. Therefore, the WHO has set a guideline value for drinking water quality concerning one congener of microcystin. Consequently, the design of a validated, public reference method to detect and quantify the hepatotoxins in drinking water is necessary. During this study, a method was developed to quantify cyanotoxins (eight microcystin congeners and nodularin) in water using liquid chromatography coupled with tandem mass spectrometry. Additionally, bottled and tap water samples were tested for the presence of cyanotoxins. No cyanotoxins were detected in any of the collected water samples. However, quality controls and the results of a proficiency test show the validity of the method.