Overreliance on agro based farm inputs to improve agricultural yield, discharge of industrial waste and lack of proper sewerage system within the towns that the lower section of Nzoia River passes through has resulted to an increased amount of pollutants being deposited into the river. With the water from the river being used for irrigation purposes, drinking by human beings and livestock as well as recreational areas, concerns have been raised on the suitability of the river to serve the above purpose as well as the safety of the produce that depend on the river. This study aimed at investigating whether the waters and sediments along lower Nzoia River have been contaminated with heavy metals. In this study, sediment and water samples were collected and analyzed. Sediment samples were collected at depths of 30 cm, 50 cm and 100 cm on either side of the river at thirty sampling sites to give a total of 180 samples as well as 60 water samples at the same points.  The collected water samples were analyzed by the use of TXRF while the sediment samples were analyzed using EDXRF. Trends in variation of concentrations with depth were evaluated as well as observing the trends in the concentration of metals downstream. The mean concentrations (mg kg-1) in sediments ranged: Mn (519 – 2064), Fe (27000 – 83000), Cu (251 – 392), Ni (262 – 509), V (150 – 384), Cr (85 – 322), Zn (43 – 100), Pb (7 – 26) and As (10 – 15). Metal concentration levels in sediment samples increased downstream with a significant variation (p < 0.05) being observed between the sampling points. The mean concentrations of Mn, Fe, Cu, Cr and Ni were above the USEPA guidelines. Metal concentrations in water samples were largely below the set guidelines except for copper that had higher amounts. The mean water concentrations reported in μg l-1 were Mn (78), Fe (6144), Ni (13.7), Cu (26.5), Zn (161) and Pb (11.2). The concentrations of heavy metals with respect to concentrations were in the order Fe > Zn > Mn > Cu > Ni > Pb. Lower river Nzoia sediments were determined to be contaminated with Mn, Fe, Cu, Cr and Ni with the concentrations  in sediments being higher than those determined for water.

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