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There is growing concern about the prevalence and impact of contaminants of emerging concern (CECs). The environmental monitoring of CECs has, however, been limited in low‐ and middle‐income countries due to the lack of advanced analytical instrumentation locally. In the present study we employed a nontargeted and suspect screening workflow via liquid chromatography coupled with high‐resolution mass spectrometry (HRMS) to identify known and unknown pollutants in the Glen Valley wastewater treatment plant, Botswana, complemented by analysis of groundwater samples. The present study represents the first HRMS analysis of CECs in water samples obtained in Botswana. Suspect screening of 5942 compounds qualitatively identified 28 compounds, including 26 pharmaceuticals and two illicit drugs (2‐ethylmethcathinone and 11‐nor‐9‐carboxy‐Δ9‐tetrahydrocannabinol). Nontargeted analysis tentatively identified the presence of 34 more compounds including (5ξ)‐12,13‐dihydroxypodocarpa‐8,11,13‐trien‐7‐one, 12‐aminododecanoic acid, atenolol acid, brilliant blue, cyclo leucylprolyl, decanophenone, DL‐carnitine, N,N′‐dicyclohexylurea, N4‐acetylsulfamethoxazole, NP‐003672, and 24 polyethylene glycol polymers. The highest number of detections were in influent wastewater (26 CECs) followed by effluent wastewater (10 CECs) and, lastly, groundwater (4 CECs). Seventeen CECs detected in the influent water were not detected in the effluent waters, suggesting reduced emissions due to wastewater treatment. Two antiretroviral compounds (abacavir and tenofovir) were detected in the influent and effluent sources. This suggests that wastewater treatment plants are a major pathway of chemical pollution to the environment in Botswana and will help inform prioritization efforts for monitoring and remediation that is protective of these key ecosystems. Environ Toxicol Chem 2024;43:52–61. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. [ABSTRACT FROM AUTHOR]