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Widespread use of pesticides globally has led to serious concerns about environmental contamination, particularly with regard to aquatic and soil ecosystems. This work involved investigating concentrations of 64 pesticides in surface-water and soil samples collected in four provinces along the Mekong River in Cambodia during the dry and rainy seasons (276 samples in total), and conducting semi-structured interviews with local farmers about pesticide use. Furthermore, an ecological risk assessment of the detected pesticides was performed. In total, 56 pesticides were detected in surface water and 43 in soil, with individual pesticides reaching maximum concentrations of 1300 ng/L in the surface-water samples (tebufenozide) and 1100 ng/g dry weight in the soil samples (bromophos-ethyl). The semi-structured interviews made it quite evident that the instructions that farmers are provided regarding the use of pesticides are rudimentary, and that overuse is common. The perceived effect of pesticides was seen as an end-point, and there was a limited process of optimally matching pesticides to pests and crops. Several pesticides were used regularly on the same crop, and the period between application and harvest varied. Risk analysis showed that bromophos-ethyl, dichlorvos, and iprobenfos presented a very high risk to aquatic organisms in both the dry and rainy seasons, with risk quotient values of 850 for both seasons, and of 67 in the dry season and 78 in the rainy season for bromophos-ethyl, and 49 in the dry season and 16 in the rainy season for dichlorvos. Overall, this work highlights the occurrence of pesticide residues in surface water and soil along the Mekong River in Cambodia, and emphasizes the urgent need for monitoring and improving pesticide practices and regulations in the region.