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High Mo concentrations have been detected in drinking water pumped from domestic water supply wells located in the Wadi Al Arab area, at the Irbid city, northern Jordan. The main objective of this study is to investigate hydrogeochemical processes responsible for the release of Mo in the groundwater resources. Usually Mo is a metallic element that is naturally present in the earth’s crust. However, the presence of Mo in groundwater is an important potential pollution issue. To achieve the objectives of the study, 34 water samples were collected from the whole catchment area of Wadi Al Arab and were analyzed using ICP-MS for total Mo and the other major cations, anions and heavy metals. The results obtained from the hydrogeochemical investigation show that the groundwater in Wadi Al Arab catchment area is susceptible to Mo contamination due to the chemical reactions of water with clay-rich underlying bedrock that consists mainly of shale and marl rocks. The concentration values measured at the tested wells vary from 46.6 μg/L to 1438.7 μg/L, with an average value of 397.6 μg/L. Therefore, about 70% of the analyzed water samples show Mo levels that exceed the permissible limit of 70 μg/L for drinking water according to World Health Organization. The results of geochemical modeling using VISUAL MINTEQ software show that the most abundant species of Mo mineral is molybdate ion (MoO42-), with a concentration of 30 μg/L, which accounts for more than 50% of the Mo species dissolved in groundwater. The possible source of the Mo in the groundwater in Wadi Al Arab catchment area is due to presence of oil shale and phosphate layers within the geological succession of the aquifer. Through the geochemical model, the saturation indices of the common Mo minerals were calculated. The calculated saturation indices showed that groundwater is under-saturated with respect to Mo mineral speciation, which emphasizes that natural equilibrium will never be reached.