A solid-phase microextraction (SPME)/gas chromatography (GC)mass spectrometry (MS) multiresidue analytical method was developed for 16 pesticides presenting different physicochemical properties including diphenyl ether, triazine, ureas, acetamides, benzofuran, thiocarbamate, pyridine carboxamides, chloronitrile, piperedine, and azoles. Optimization was achieved by means of the design of experiments methodology. Extraction temperature, extraction time, desorption temperature, and NaCl addition were the factors exhibiting the most significant effects on pesticide extraction. Validation was carried out through model adequacy and specificity tests, limits of quantification and detection determination, and full uncertainty assessment on the whole analytical method. Good first- and second-order model adequacy was found for pesticide calibration. LOQs were in the 0.050.5 μg L−1 range and specificity recoveries varied from 75% to 140%. These results were considered acceptable for our research purposes on highly concentrated agricultural flows. Uncertainty calculations accounted for several steps: standard preparation, calibration model selection, and use. On average, real sample concentration uncertainties were lower than 10%, indicating that the analytical method performed very well. Its application to 61 real water samples confirmed the presence of some pesticide concentrations in relation to farmer use, whereas other molecules were usually either not detected or not quantified.