Water is an essential resource for all living organisms. The continuous and increasing use of pesticides in agricultural and urban activities results in the pollution of water resources and represents an environmental risk. To control and reduce pesticide pollution, reliable multi-residue methods for the detection of these compounds in water are needed. In this context, the present work aimed at providing an analytical method for the simultaneous determination of trace levels of 51 target pesticides in water and applying it to the investigation of target pesticides in two agriculture-impacted areas of interest. The method developed, based on an isotopic dilution approach and on-line solid-phase extraction-liquid chromatography-tandem mass spectrometry, is fast, simple, and to a large extent automated, and allows the analysis of most of the target compounds in compliance with European regulations. Further application of the method to the analysis of selected water samples collected at the lowest stretches of the two largest river basins of Catalonia (NE Spain), Llobregat and Ter, revealed the presence of a wide suite of pesticides, and some of them at concentrations above the water quality standards (irgarol and dichlorvos) or the acceptable method detection limits (methiocarb, imidacloprid, and thiacloprid), in the Llobregat, and much cleaner waters in the Ter River basin. Risk assessment of the pesticide concentrations measured in the Llobregat indicated high risk due to the presence of irgarol, dichlorvos, methiocarb, azinphos ethyl, imidacloprid, and diflufenican (hazard quotient (HQ) values>10), and an only moderate potential risk in the Ter River associated to the occurrence of bentazone and irgarol (HQ>1).