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The need for clean and safe consumable water is of paramount importance to any society since water is a crucial substance for the sustenance of life. Kibera slum is one of the leading slums in the world with a high population, leading to poor levels of sanitation and inadequate clean water supply. Consequently, the residents have to seek for alternative water supply. Motoine River flows through the slum, and thus acts as an alternative source of water. This study determined the concentration levels of heavy metals (Pb, Fe, Cu, Cr and Cd) and nutrients (nitrates, nitrites and phosphates) in Motoine River, Kibera in September 2014 and compared the variations downstream. The metals were determined using Atomic Absorption Spectroscopy (AAS) while the nutrients were determined using UV/Visible spectroscopy. Concentration levels of Cu, Cd and Cr were found to be lower than the Environmental Protection Agency (EPA) values for maximum contaminant level (MCL) while those of Fe, Pb and the nutrients were higher than EPA’s MCL values. Cd had the lowest concentration and was below the detection limit of the instrument used. Nitrates were found to be of the highest concentration at 16.4959 ± 2.4432 parts per million (ppm). The high concentration of nutrients in the water could be due to domestic waste and effluent disposal into the river and agricultural runoffs while that of metal ions could be due to waste from informal jua kali industries and erosion of natural deposits. The efforts by the government to rehabilitate and clean rivers within Nairobi should be extended to include Motoine River.