A method based on sequential stir bar sorptive extraction followed by automated thermal desorption-GC-MS for the determination of pesticides in underground and superficial water samples has been developed. Retention time locked GC-MS and deconvolution Automated Mass Spectral Deconvolution and Identification System software allows the use of pesticide databases for identification and quantification in routine applications. Quantitation limits and repetitivity using full scan mass spectrometric determination guarantee the applicability of the method, which enables considerable savings to be made in total analysis time, with data processing times of around 2 min/sample.