This study focused on the input of hydrophilic biocides into the aquatic environment and on the efficiency of their removal in conventional wastewater treatment by a mass flux analysis. A fully automated method consisting of on-line solid phase extraction coupled to LC-ESI-MS/MS was developed and validated for the simultaneous trace determination of different biocidal compounds (1,2-benzisothiazoline-3-one (BIT), 3-Iodo-2-propynylbutyl-carbamate (IPBC), irgarol 1051 and 2-N-octyl-4-isothiazolinone (octhilinone, OIT), carbendazim, diazinon, diuron, isoproturon, mecoprop, terbutryn and terbutylazine) and pharmaceuticals (diclofenac and sulfamethoxazole) in wastewater and surface water. In the tertiary effluent, the highest average concentrations were determined for mecoprop (1010 ng/L) which was at comparable levels as the pharmaceuticals diclofenac (690 ng/L) and sulfamethoxazole (140 ng/L) but 1–2 orders of magnitude higher than the other biocidal compounds. Average eliminations for all compounds were usually below 50%. During rain events, increased residual amounts of biocidal contaminants are discharged to receiving surface waters.