Heavy metal contamination in surface waters is a significant global concern, particularly because people often settle near accessible water sources like lakes. This study examined the concentrations of heavy metals in water from selected locations along the shores of Lake Turkana and Turkwel River using Microwave Plasma Atomic Emission Spectroscopy (MPAES). In Lake Turkana, arsenic had the highest overall average concentration (0.756 mg/l) while Cd had the lowest (0.013mg/l) while in River Turkwel Zn had the highest average concentration (0.847 mg/l) with Cr being lowest (0.012mg/l). The Metal Contamination Index (MCI) in both the Lake and the River water was 0.001, while the corresponding Heavy metal Evaluation Indices (HEI) were 94.171 and 93.626 respectively. Concentrations of Cd, Ni, As, Pb and Cr were higher in the current study compared to the WHO recommended levels for drinking water.