GC-MS/MS is widely used for trace-level pesticide analysis in various samples, however, thermal degradation and adsorption on active sites of the chromatographic system remain major challenges. In this study, a multiresidue method using automated SPE-GC-MS/MS was optimized for the determination of 67 pesticides in treated and raw water. A systematic study of the use of analyte protectants, gluconolactone and D-sorbitol, showed that at appropriate concentrations, they deactivated active sites of the GC-MS/MS system, resulting in sharper peaks, improved sensitivity and lower detection limits. Some analytes did not even have an analytical signal when analyte protectors were not used. A thorough study of the matrix effect on several pesticide classes demonstrated that analyte protectants effectively compensated for matrix suppression in carbamates and triazines, though matrix-matched calibration remained necessary for other classes. The method validation, conducted under SANTE/2020/12830 guidelines, yielded limits of quantification between 0.010 and 0.080 μg L-1, recovery ranging from 81 to 120 %, and RSDs below 20 %. Environmental sample analysis revealed pesticide residues in 28 % of water samples, including azoxystrobin, a fungicide listed on the European Union Watch List.