The monitoring of freshwaters regarding organic micropollutants such as pesticides requires efficient analytical methods to determine reliable concentrations at low levels in natural waters. In this aim, two complementary methods were developed for the determination of several pesticides in surface waters using Stir Bar Sorptive Extraction (SBSE) followed by liquid chromatography or gas chromatography coupled to tandem mass spectrometry. These two methods were validated and their analytical uncertainties were determined according to French standards. Linearity and limits of quantification (LOQ) were statistically tested and the efficiency, repeatability and expanded uncertainties were evaluated for each compound. The SBSE-TD-MS-MS method achieved lower LOQ although the number of compounds analyzed was lower than for the SBSE-LD-UHPLC-MS-MS method.