Water is a fundamental resource for living things, which is why its control is necessary. The widespread use of pesticides for agricultural and non-agricultural purposes has resulted in the presence of their residues in surface water and groundwater resources. Their presence in water is regulated through different directives, such as the Groundwater Directive, the Drinking Water Directive, and the Water Framework Directive, modified later several times, setting a maximum concentration of 0.1 µg.L−1for individual pesticides and their degradation products, and 0.5 µg.L−1for total pesticide residues present in a sample. There are different kinds of pesticides (e.g., organophosphorus and organochlorine pesticides, triazines, chloroacetamides, triazoles, (thio)carbamates) that have diverse chemical structures. Their determination and monitoring in a single analytical procedure are possible through multiresidue methods. In this study, 53 pesticides belonging to different chemical classes and their metabolites were selected based on their local occurrence and investigated in surface water and groundwater from agricultural areas susceptible to pesticide contamination. The methodology consisted of a classical solid-phase extraction (SPE) for the purification and enrichment of the pesticides, with a subsequent analysis in multidimensional gas chromatography coupled to mass spectrometry (GC×GC-MS). The quantification method was validated according to the Eurachem Guide in terms of linearity, precision, accuracy, limit of detection, and limit of quantification. After validation, the method was applied to 34 real-world water samples, and the results were compared with those obtained by a GC-QMS routine method.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00216-023-04686-8.