Emerging organic contaminants have not received a lot of attention in developing countries, particularly Africa, although problems regarding water quantity and quality are often even more severe than in more developed regions. This study presents general water quality parameters as well as unique data on concentrations and loads of 24 pharmaceuticals including antibiotic, anti(retro)viral, analgesic, anti-inflammatory and psychiatric drugs in three wastewater treatment plants, three rivers and three groundwater wells in Nairobi and Kisumu. This allowed studying removal efficiencies in wastewater treatment, identifying important sources of pharmaceutical pollution and distinguishing dilution effects from natural attenuation in rivers. In general, antiretrovirals and antibiotics, being important in the treatment of common African diseases such as HIV and malaria, were in all matrices more prevalent as compared to the Western world. Wastewater stabilization ponds removed pharmaceuticals with an efficiency between 11 and 99%. Despite this large range, a different removal is observed for a number of compounds, as compared to more conventional activated sludge systems. Total concentrations in river water (up to 320 μg L(-1)) were similar or exceeded concentrations in untreated wastewater, with domestic discharges from slums, wastewater treatment plant effluent and waste dumpsites identified as important sources. In shallow wells situated next to pit latrines and used for drinking water, the recalcitrant antiretroviral nevirapine was measured at concentrations as high as 1-2 μg L(-1). Overall, distinct pharmaceutical contamination patterns as compared to the Western world can be concluded, which might be a trigger for further research in developing regions.