In order to assess the pollution levels of selected heavy metals, 45 bottom sediment samples were collected from Al-Kharrar lagoon in central western Saudi Arabia. The concentrations of the heavy metals were recorded using inductively coupled plasma-mass spectrometer (ICP-MS). The results showed that the concentrations of Pb and Cd exceeded the environmental background values. However, the heavy metal contents were less than the threshold effect level (TEL) limit. The concentrations of heavy metals in lagoon bottom sediments varied spatially, but their variations showed similar trends. Elevated levels of metals were observed in the northern and southern parts of the lagoon. Evaluation of contamination levels by the sediment quality guidelines (SQG) of the US-EPA revealed that sediments were non-polluted-moderately to heavily polluted with Pb; non-polluted to moderately polluted with Cu; and non-polluted with Mn, Zn, Cd, and Cr. The geoaccumulation index showed that lagoon sediments were unpolluted with Cd, Mn, Fe, Hg, Mo, and Se; unpolluted to moderately polluted with Zn and Co; and moderately polluted with Pb, Cr, Cu, and As. The high enrichment factor values for Pb, As, Cu, Cr, Co, and Zn (>2) indicate their anthropogenic sources, whereas the remaining elements were of natural origins consistent with their low enrichment levels. The values of CF indicate that the bottom sediments of Al-Kharrar lagoon are moderately contaminated with Mn and Pb.