The aim of this study is to determine the types of heavy metals frequently present in Makkah wells and the possible environmental causes of their distribution and accumulation. Makkah lies in a mountain range dominated by different types of rocks from the Precambrian and Lower Paleozoic eras, as well as subordinate sedimentary rocks and basaltic lava flow from the Tertiary and Quaternary periods. Natural contaminants in Makkah wells water can be attributed to the unique location. Many epidemiological studies have identified associations between the ingestion of wells water contaminated with heavy metals and increased risk of some illnesses. This study presents exclusive information on the levels and distribution of 9 heavy metals—arsenic, barium, cadmium, chromium, cobalt, copper, lead, mercury, and selenium—in the wells water in various rural and urban areas of Makkah city. These naturally occurring elements are considered significant markers of water purity. More than 160 wells were involved in this three-year investigation. Water samples were collected during different seasons in order to assess any changes in the distribution and concentration of these heavy metals throughout the year. The collected water samples were filtered and digested before analysis using inductively coupled plasma mass spectrometry (ICP/MS). We found the following sequence of concentrations of heavy metals in the studied wells: Ba > Se >Cr > As > Co > Cu> Hg > Pb > Cd. Arsenic, barium, chromium, and selenium were the most abundant contaminants in the wells studied. The concentrations of the other heavy metals ranged from non-detectable to 3 μg/L. Although low, these values are also reported in comparisons with the local and international strict values and standards which govern the maximum contaminant levels permitted for long-term daily consumption.