Wastewater contains a variety of chemical substances owing to the different sources that contribute to affluent into sewage treatment plants. Raw and wastewater samples were obtained from the surface of the water bodies at depths of 50 and 100 metres but at different locations in each sampling site. The water samples were subjected to extraction of polychlorinated biphenyls (PCBs) using QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) extraction kit before analysis using the Gas Chromatography Mass Spectrometer (GC-MS). The control samples had turbidity, temperature and pH values within the acceptable levels as per Botswana, South Africa and WHO drinking water standards. Turbidity values were rather higher than the set standards for raw and wastewater, with water samples from Modimola/Setumo dam having recorded the highest range of 25.0 – 200 Nephelometric Turbidity Units (NTU). The same sampling site also had water samples with pH higher at 9.01 to 9.78. Wastewater effluent in Notwane Sewage Treatment Plant, Gaborone Dam (both in Gaborone) and Disaneng Dam (South Africa) have polychlorinated biphenyls (PCBs) below detectable levels by the Agilent Gas Chromatography Mass Spectrometer (GC-MS). Only traces of PCBs were detected from wastewater from Modimola dam in Mafikeng. This may be due to the different industries in Mafikeng producing various chemicals compared to Gaborone. The water in Modimola dam therefore requires thorough treatment before it can be returned for domestic consumption as PCBs are toxic compounds that are found to trigger cancer in humans and also affect the reproduction system resulting in low IQ.