The largely uncontrolled release of active pharmaceuticals ingredients (APIs) within untreated wastewater discharged to waterbodies, associated with many rapidly urbanising centres is of growing concern owing to potential antimicrobial resistance, endocrine disruption and potential toxicity. A sampling campaign has been undertaken to assess the source, occurrence, magnitude and risk associated with APIs and other chemicals within the Nairobi/Athi river basin, in Kenya, East Africa. The catchment showed an extensive downstream impact zone estimated to extend 75 km, mostly, but not exclusively, derived from the direct discharge of untreated wastewater from the urban centre of Nairobi city. The exact extent of the downstream boundary of the Nairobi city impact zone was unclear owing to the inputs of untreated wastewater sources from the continuous urbanized areas along the river, which counteracted the natural attenuation caused by dilution and degradation. The most frequently detected APIs and chemicals were caffeine, carbamazepine, trimethoprim, nicotine, and sulfamethoxazole. Paracetamol, caffeine, sulfamethoxazole, and trimethoprim alone contributed 86% of the total amount of APIs determined along the Nairobi/Athi catchment. In addition to direct discharge of untreated domestic wastewater attributed to the informal settlements within the conurbation, other sources were linked to the industrial area in Nairobi City where drug formulation is known to occur, the Dandora landfill and veterinary medicines from upstream agriculture. It was shown that there was a possible environmental risk of API ecotoxicological effects beyond the end of the traditional impact zone defined by elevated biochemical oxygen demand concentrations; with metronidazole and sulfamethoxazole exhibiting the highest risk.