Many rivers in urbanised catchments in South Africa are polluted by raw sewage and effluent to an extent that their ecological function has been severely impaired. The Hennops and Jukskei Rivers lying in the Hartbeespoort Dam catchment are two of the worst impacted rivers in South Africa and are in need of rehabilitation. Passive sampling (Chemcatcher® with a HLB receiving phase) together with high-resolution tandem mass spectrometry–targeted screening was used to provide high sensitivity and selectivity for the identification of a wide range of emerging pollutants in these urban waters. Over 200 compounds, including pesticides, pharmaceuticals and personal care products, drugs of abuse and their metabolites were identified. Many substances (~ 180) being detected for the first time in surface water in South Africa. General medicines and psychotropic drugs were the two most frequently detected groups in the catchment. These accounted for 49% of the emerging pollutants found. Of the general medicines, antihypertensive agents, beta-blocking and cardiac drugs were the most abundant (28%) classes detected. The Hennops site, downstream of a dysfunctional wastewater treatment plant, was the most polluted with 123 substances detected. From the compounds detected, peak intensity–based prioritisation was used to identify the five most abundant pollutants, being in the order caffeine > lopinavir > sulfamethoxazole > cotinine > trimethoprim. This work provides the largest available high-quality dataset of emerging pollutants detected in South African urban waters. The data generated in this study provides a solid foundation for subsequent work to further characterise (suspect screening) and quantify (target analysis) these substances.