In this study, the levels of natural and anthropogenic metal contamination (aluminum (Al), iron (Fe), manganese (Mn), arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), and zinc (Zn)) in surface sediments of three harbors along the Iranian coast of Gulf of Oman were examined and reported for the first time. Effect of grain size, mineralogy, normalization technique using Fe concentrations, and different sediment quality guidelines were discussed. Data from the harbors were compared with other harbors worldwide. Sediments inside the harbors are characterized by moderate and high levels of pollution by trace metals Cu (12-287 μg/g), Pb (11-1,780 μg/g), Zn (38-547 μg/g), Cr (70-2,370 μg/g), and Ni (31-116 μg/g). However, As and Cd did not show considerable pollution inside and outside the harbors. Considering that there is no industrial activity around the study harbors, the major sources of contamination in the harbors are repairing, fueling, greasing, and painting of fishing ships and boats. Mineralogy of sediments in the study area as well as trace metal concentration in reference samples taken from onshore geological units confirmed that natural inputs of Cd, Cu, Pb, and Zn in the harbors are very low while most of Ni and Cr contamination in the study area comes from erosion of ophiolitic mélange units at the North of Makran mountains.