Pesticides are substances used to prevent, control, or eliminate pests, weeds, and other harmful organisms in agricultural and non-agricultural settings. The use of pesticides in intensive agricultural areas of Cambodia poses significant risks of pollution of groundwater resources. This study investigates pesticide residues in groundwater from Koh Thum district, Kandal Province, and Kanghot area, Battambang Province. Five groundwater sampling sites in Koh Thum and five in Kanghot were collected from existingtube wells and push points with the water level ranges from 0.16 m to 20 m and shallow to intermediate-depth groundwater systems. The groundwater samples were processed using solid-phase extraction and analyzed by gas chromatography-mass spectrometry equipped with an automated system (451-compound database) to identify and quantify pesticide residues in groundwater samples. The results revealed detectable residues of atrazine, parathion chlorfenapyr, metalaxyl and azoxystrobin in the groundwater samples from Koh Thum while metalaxyl, chlorfenapyr and spirodiclofen were detected in the groundwater samples from Kanghot. Several groundwater samples from Koh Thum district exceeded the European Union guideline value of 0.1 µg/L for individual pesticides, and one sample exceeded the guideline limit of 0.5 µg/L for total pesticide concentration. In contrast, a few groundwater samples from the Kanghot area also exceeded this guideline of individual compound. Chlorfenapyr was the most frequently detected pesticide and showed the highest concentration. The detection of atrazine at a water level of 20 m and other pesticides at water levels ranging from 0.16 to 17.2 m suggests the transport of pesticide residues from agricultural soils to groundwater. The concentration of these pesticides highlights potential contamination from agricultural runoff, raising concerns about chronic exposure risks for communities. Overall, the findings highlight the urgent need for systematic groundwater monitoring, stricter pesticide regulation, and improved management practices to support sustainable agriculture and protect human health in Cambodia’s intensively farmed regions.