The study was carried out in six Kenyan rift valley lakes, Nakuru, Magadi, Oloiden, Crater (Sonachi), Bogoria and Elementaita with the aim to determine the levels of heavy metals and other metal elements (Co, Mn, Zn, Cu, Cr, Cd, Pb, Ni, Hg and As) in water and sediment samples as well as assess its association with water bird distribution. High levels of Pb (42 ppm) above the Pb benchmark levels (36 ppm) as per EPA (2007) benchmarks were detected in Lake Oloiden sediments. Lakes Bogoria and Elementaita had high levels of Mn (3676.7 ± 6652.3 and 747.55 ± 510.95, respectively), also above the Mn benchmark levels (631 ppm), according to EPA (2007). The mean sediment concentrations for Zn, Pb, Ni, As and Hg varied significantly (P 0.05). It was concluded that metals concentration in Kenyan Rift Valley lakes has no significant influence on the distribution of water birds. High Mn levels in lakes Bogoria and Elementaita, and Pb in Oloiden may cause toxic effects to the aquatic life and humans as a result of bioaccumulation. Key words: Ecotoxicology, heavy metals, water birds.