The agriculturally dominated region of the Western Cape, South Africa is vulnerable to pesticide pollution. A 2017–2019 pesticide monitoring campaign in the agricultural catchments of Grabouw, Piketberg and Hex River Valley identified year-round detections despite few agricultural applications, making pesticide pollution sources unclear. To better trace pesticide sources in these catchments, our study measured 19 pharmaceutical compounds and one industrial chemical as an indicator for wastewater treatment plant (WWTP) effluent - in addition to 44 pesticides. Passive samplers were deployed monthly in rivers from February 2022 to March 2023 in Grabouw, Hex River Valley, and Piketberg, and one control sample in Jonkershoek Nature Reserve (May 2022). Some pesticides without year-round agricultural applications had high detection frequencies and Groundwater Ubiquity Scores, suggesting leaching of pesticides into groundwater connected to rivers. Cumulative pharmaceutical concentrations correlated strongly with cumulative pesticide concentrations only in the Piketberg catchment, suggesting WWTPs as a possible pesticide source. Herbicide detections in Jonkershoek Nature Reserve (e.g., atrazine) suggest contamination from atmospheric transport, invasive plant control or trail maintenance. The Environmental Quality Standard (EQS) for imidacloprid, chlorpyrifos, terbuthylazine and spiroxamine was exceeded at least once during the 1-year monitoring period, mostly related to expected agricultural applications, indicating high persistence and continuous exposure risk to aquatic organisms. Our study is the first to describe the relevance of WWTPs as a pesticide source in South African agricultural catchments. Drivers of pesticide contamination were area dependent, emphasizing the need for catchment-specific understanding. Future research requires sampling of groundwater and wastewater influent and effluent to improve our understanding of pesticide transport pathways and sources.