Background In South Africa there is little data on environmental pollution of rural water sources by agrochemicals. Methods This study investigated pesticide contamination of ground and surface water in three intensive agricultural areas in the Western Cape: the Hex River Valley, Grabouw and Piketberg. Monitoring for endosulfan and chlorpyrifos at low levels was conducted as well as screening for other pesticides. Results The quantification limit for endosulfan was 0.1 μg/L. Endosulfan was found to be widespread in ground water, surface water and drinking water. The contamination was mostly at low levels, but regularly exceeded the European Drinking Water Standard of 0.1 μg/L. The two most contaminated sites were a sub-surface drain in the Hex River Valley and a dam in Grabouw, with 0.83 ± 1.0 μg/L (n = 21) and 3.16 ± 3.5 μg/L (n = 13) average endosulfan levels respectively. Other pesticides including chlorpyrifos, azinphos-methyl, fenarimol, iprodione, deltamethrin, penconazole and prothiofos were detected. Endosulfan was most frequently detected in Grabouw (69%) followed by Hex River (46%) and Piketberg (39%). Detections were more frequent in surface water (47%) than in groundwater (32%) and coincided with irrigation, and to a lesser extent, to spraying and trigger rains. Total dietary endosulfan intake calculated from levels found in drinking water did not exceed the Joint WHO/FAO Meeting on Pesticide Residues (JMPR) criteria. Conclusion The study has shown the need for monitoring of pesticide contamination in surface and groundwater, and the development of drinking water quality standards for specific pesticides in South Africa.