A robust method is provided to analyze 18 hydrophilic and hydrophobic biocides in both dissolved and particulate fractions of five types of urban and surface waters using high performance liquid chromatography coupled to tandem mass spectrometry. The linearity, accuracy and intermediate precision were validated. The target biocides were enriched by solid phase extraction using Chromabond HR-X 200 mg cartridges and eluted with methanol, ethyl acetate and dichloromethane. Suspended matter was extracted by microwave-assisted extraction in methanol and dichloromethane. Recoveries and variability (respectively >75% and < 30% for most of the target biocides and matrices) made it possible to quantify biocides at trace level in all matrices. LOQs were in the range of ng/L in the dissolved fraction and in the range of ng/g.dw in the particulate fraction for most of the biocides and matrices and were generally lower than those reported in previous studies. The method was successfully applied to surface water, treated and untreated wastewater, combined sewer overflows, and stormwater providing, unique data in these matrices for some substances, in particular with respect to particle contamination. In urban waters, concentrations of most of the biocides ranged from 10 to 200 ng/L. Diuron, isothazolinone and benzalkonium concentrations could reach 0.9, 0.9 and 20 µg/L respectively. In rivers, most of the biocides were measured at less than 10 ng/L, but higher concentrations were observed for benzalkoniums (up to 200 ng/L) or after rain events, which indicates biocide transfer from urban surfaces into the aquatic environment during wet weather.