The need for clean and safe consumable water is of vital importance to any society since water is an essential substance for the sustenance of life. Mogadishu is one of the rapidly growing cities in the world with a high population, resulting in poor levels of sanitation and an inadequate clean water supply system. A total of 6 water samples were analyzed from the Mogadishu region in seven sites namely, Rer M.Shiekh, Gorgor, Umu batula, Cisse qodax, Soonikia (digfer), and Tarabuuna (umu caisha) respectively to assess the levels of heavy metals. The levels of selected heavy metals analyzed were Cd, Zn, and Pb, the analysis was done by Atomic Absorption Spectrophotometer and other parameters analyzed were the level of pH, fluoride, chloride, nitrate, water hardness, electrical conductivity, and total dissolved solids (TDS), and the status of water borehole quality in the Southern Mogadishu region, Somalia. The results were compared with World Health Organization (WHO). pH values ranged (8.1-8.9) which were below WHO standard limits except for Cisse qodax borehole (8.9) which was higher than WHO standard limits. Other value for parameters were fluoride (0.28-0.596 mg/L); chloride (279.57-888.92 mg/L); nitrate (4.27-146.6 mg/L); electrical conductivity (1.428-3.280 mS /cm); hardness (229.32-501.76 mg/L); total dissolved solids (1340-3428 mg/L); cadmium (0.03-0.07 mg/L). Lead and zinc were not detected. Hardness, chloride, electrical conductivity, total dissolved solids (TDS), cadmium values were higher than WHO standard limits. Nitrate values were below WHO standard limits except for Umu batula borehole (60.92 mg/L) and Rer M.shiekh borehole (146.6 mg/L) which are values higher than WHO standard limits. All boreholes had low fluoride content. However high cadmium concentration is of much concern health-wise. The presence of heavy metals in the water borehole is of concern since they could impact negatively on human health even at low levels due to their accumulation. This study is of significance in providing information on the heavy metals content of the selected water boreholes in Mogadishu, information that is currently lacking considering the management issues in the Country. Further, it could help in mapping out the boreholes based on their water quality.