Heavy metal pollution in surface water of four lakes (Naivasha, Elementaita, Nakuru, and Bogoria) of the Great Rift Valley in Kenya, East Africa was investigated in this study. Eight heavy metals including chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), lead (Pb), cadmium (Cd), and mercury (Hg) were determined using inductively coupled plasma-mass spectrometer (ICP-MS). Among the tested heavy metals, Cd and Hg were detected in all surface water samples. The concentrations of Cr, Cd, Ni, and Pb were relatively lower than those of other metals in the four lakes. Results of Kohonen self-organizing map indicated that all the sampling sites in four lakes of the Great Rift Valley in Kenya could be classified into three different groups based on the heavy metal pollution. Lake Naivasha and Nakuru had characteristics of low concentrations of Cr, Ni, Cu, As, and Hg. Lake Bogoria was characterized by high levels of Ni, Cu, Cd, and Hg, and low levels of Pb, Cr, Zn, and As. Lake Elementaita showed characteristics of high concentrations of As and Hg and low concentrations of Pb, Ni, Cu, and Cd. Source identification using principal component analysis (PCA) indicated that anthropogenic factor played an increasingly important role in the heavy metal pollution of four lakes of the Great Rift Valley in Kenya, East Africa. Analysis of non-carcinogenic health risks of heavy metals indicated Hg and As in Lake Elementaita and Hg in Lake Bogoria may pose adverse health effects to local residents via ingestion route.