Due to human population increase, industrialization, use of fertilizers in agriculture and human-made activities, our bodies of water can be polluted with heavy metals such as lead. The aim of this study was to assess lead contamination in the waters of the Port of Mukas, Kolambugan, Lanao del Norte. Three sampling stations were established in the area and collection of water samples was done in replicates. The presence of lead was determined using atomic absorption spectroscopy. Results showed that the average lead concentration was 0.18 mg/L which exceeds the allowable limit value of 0.5 mg/L set by the Department of Environment and Natural Resources for toxic and deleterious substances in marine waters with beneficial usage. The high concentration of lead in the area might be due to the salvaging of ships which uses paints and welding equipment as well as leaded petrol cars and some discharges from industries and residential houses near the port. The results of this study may serve as baseline information for developing and implementing conservation policies or strategies to effectively manage the aquatic environment of the Port of Mukas and the Panguil Bay at large.