Pesticides residues in aquatic ecosystems are an environmental concern which requires efficient analytical methods. In this study, we proposed a generic method for the quantification of 13 pesticides (azoxystrobin, clomazone, diflufenican, dimethachlor, carbendazim, iprodion, isoproturon, mesosulfuron-methyl, metazachlor, napropamid, quizalofop and thifensulfuron-methyl) in three environmental matrices. Pesticides from water were extracted using a solid phase extraction system and a single solid-liquid extraction method was optimized for sediment and fish muscle, followed by a unique analysis by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Limits of quantification were below 5 ng L−1 for water (except for fluroxypyr and iprodion) and ranged between 0.1 ng g−1 and 57.7 ng g−1 for sediments and regarding fish, were below 1 ng g−1 for 8 molecules and were determined between 5 and 49 ng g−1 for the 5 other compounds. This method was finally used as a new routine practice for environmental research.