The Guanajuato mining district has had mining operations for over 500 years. This mining district is one of the most important Ag-Au producers in Mexico and is among the largest deposits in the world. The natural enrichment of heavy metals and metalloids (HM&Ms) in the Guanajuato River basin (GRB), and the different mineral recovery methods used over time have caused relatively high concentrations in stream sediments and soil, posing a potential risk to the environment. This study conducted column experiments to evaluate the potential of HM&Ms leaching from the soil into the groundwater upstream of GRB. The column experiment results were modeled (inverse modeling) in PHREEQC in order to analyze the soilwater interaction. Inverse modeling determined that pH, redox conditions, mineralogy phases, and cation exchange control the mobility of HM&Ms. Soils in GRB have the potential to release Zn > Cu > Pb > Ni in low concentrations (<1mg/L) due to the stability of mineral phases and alkaline pH. However, soil leachates can precipitate clays and oxyhydroxides, which, at alkaline pH, increase their retention capacity, controlling the leachability of HM&Ms. Clay minerals present the major phases in the leaching processes, followed by carbonates and sulfides. This research demonstrated that mineralogy is the main factor influencing the availability of HM&Ms in the groundwater of the Guanajuato River Basin.