A method based on isotope dilution gas chromatography/mass spectrometry (GC/MS) with automated solid-phase extraction (SPE) is described for the analysis of 32 pesticides and metabolites in surface waters. This approach consist in the use of nine isotopically labelled representative pesticides as internal standards, which allows high accuracy (trueness and precision) and sensitivity for most analysed compounds, as it is required for isotope dilution-based methods. Uncertainties associated with pesticide determination in real samples were estimated using quality assurance/quality control (QA/QC) data. For most pesticides expanded uncertainty was below 40%, according to the commonly established requirements for analytical results. Ninety three Spanish surface waters collected in June-July and September-November 2004 were analysed. Concentration and occurrence of pesticides were evaluated. These parameters were higher in the summer than in the autumn period. In summer four pesticides were found in more than 50% of the analysed samples and four compounds were detected above the concentration level of 1 microg/l (atrazine, terbutylazine, 3,4-dichloroaniline and fenitrothion), while in autumn percentage of detection was below 50% for all pesticides and only one compound (terbutylazine) exceeded 1 microg/l.