HPLC-MS/MS was preferred over GC-MS for the analysis of the herbicides glyphosate, mecoprop, MCPA, isoproturon, bentazon and chloridazon and the metabolites aminomethylphosphonic acid (AMPA), chloridazon-desphenyl and chloridazon-methyl-desphenyl in water samples. The occurrence of the target compounds in the Baltic estuarine water was studies in 2012. Glyphosate and AMPA were the most frequently detected compounds with concentrations reached up to µg/L in some samples. Nodularia spumigena showed tolerance to Glyphosate (Roundup®) and AMPA when exposed to concentrations between 1-500 µg/L.