The analysis of pesticides in water samples is a problem of primary concern for quality control laboratories due to the toxicity level of these compounds and their public health risk. In order to evaluate the impact of pesticides in the Lisbon drinking water supply system, following the requirements of the European Union Directive 98/83/EC, we developed and validated an analytical method based on the combination of solid-phase extraction with liquid chromatography and tandem mass spectrometry. In this work, several pesticides were studied: imidacloprid, dimethoate, cymoxanil, carbendazime, phosmet, carbofuran, isoproturon, diuron, methidathion, linuron, pyrimethanil, methiocarbe, tebuconazole and chlorpyrifos. Several parameters of the electrospray source were optimized in order to get the best formation conditions of the precursor ion for each pesticide, namely capillary and extractor voltage, cone voltage, cone gas flow rate and desolvation gas flow rate. After optimization of the collision cell energy of the triple quadrupole, two different precursor ion-product ion transitions were selected for each pesticide, one for quantification and one for qualification, and these ions were monitored under time-scheduled multiple reaction monitoring (MRM) conditions. The selection of specific fragment ions for each pesticide guarantees a high degree of selectivity as well as additional sensitivity to quantify trace levels of these pesticides in water samples. This method showed excellent linearity ranges for all pesticides, with correlation coefficients greater than 0.9989. Determination limits (between 0.0041 and 0.0480 microg/L), precision (RSD <9.18%), accuracy and recovery studies in several water samples using solid-phase extraction were also performed.