In Vietnam, the continuous increasing of agricultural productions leads to an increase of the use of chemicals. Food safety becomes a subject of concern for both customers and scientists, especially because of residues of chemicals added to food during producing and processing steps. According to the survey result of the Deltaquasafe project, three pesticides were identified, which were popularly used in the Mekong delta, which are dichlorvos, quinalphos and trifluralin. In order to determine the presence of residues of these compounds in water, an analytical method was developed based on the GC-MS technique (Gas Chromatography with Mass Spectrometry detection). The analytical instrument was a Thermo Focus GC with a Thermo Polaris Q MS, and a Finnigan auto-sampler. An Equity 5 Column (30m x 0.25 mm x 0.25 àm film thickness) was used as stationary phase. The method was operated with 25 ml of water sample and extraction solvents were ethyl acetate: chloroform (1:1). Extraction was performed twice under 300 rpm shaking, during 20 minutes. After extraction the analytes were dissolved in acetone and injected to GC-MS, together with calibration curves. The LOD and LOQ of the method were 0.16 and 0.55 pg/uL for Dichlorvos, 0.09 and 0.30 pg/uL for quinalphos, 0.01 and 0.04 pg/uL for trifluralin, respectively. The method was then applied for water samples collected from rice-fish, catfish and red tilapia systems in Mekong Delta. The results showed that only 15% of water from rice fish system contained residues of quinalphos in trace amount (below the LOQ). The other pesticides were not detected.