Recently, there has been an increased interest in bridging the knowledge gap in the occurrence and fate of pharmaceuticals in African urban water cycles. In this study, the occurrence of 7 antibiotics and 3 antiretrovirals in source-separated urine, groundwater, wastewater and surface water of the peri-urban area of Chunga in Lusaka, Zambia, was studied. In groundwater, the pharmaceuticals were only sporadically present with 4 antibiotics and 1 antiretroviral detected. The concentration of the antibiotics ranged from below limit of quantification (<LOQ) to 880 ng/L, with sulfamethoxazole having the highest detection frequency of 42.3%. In the surface water, a comparatively high concentration of pharmaceuticals was measured with concentrations ranging from <LOQ–11 800 ng/L to <LOQ–49 700 ng/L for antibiotics and antiretroviral drugs, respectively. Similarly, the concentration of antibiotics in wastewater treatment plant (WWTP) influent and effluent waters ranged from 100–33 300 ng/L and 80–30 040 ng/L, respectively. The concentration of the antiretrovirals was also relatively high in the wastewater and ranged from 680–118 970 ng/L and 1 720–55 760 ng/L in the influent and effluent, respectively. The concentration of the target analytes in source-separated urine were several orders of magnitude higher than in wastewater. Sulfamethoxazole, trimethoprim and lamivudine had the highest concentrations, of 7 740 µg/L, 12 800 µg/L and 10 010 µg/L, respectively. The high concentration detected in source-separated urine calls for precautionary measures to be undertaken when such urine is to be used as a fertilizer. However, urine source separation has a major advantage of pooling a significant proportion of excreted pharmaceuticals into small manageable volumes which can be effectively treated, minimizing environmental contamination. The high concentrations of antibiotics and antiretroviral drugs measured in this study necessitate creation of effective barriers to mitigate the possible environmental and human health risks.