The modeling of ion exchange processes could significantly enhance their applicability in mine water treatment, as the modern synthetic resins give unique advantages for the removal of metals. Accurate modeling improves the predictability of the process, minimizing the time and costs involved in laboratory column testing. However, to date, the development and boundary conditions of such ion exchange systems with complex mine waters are rarely studied and poorly understood. A representative ion exchange model requires the definition of accurate parameters and coefficients. Therefore, theoretical coefficients estimated from natural exchange materials that are available in geochemical databases often need to be modified. A 1D reactive transport model was developed based on PhreeqC code, using three case scenarios of synthetic mine waters and varying the operating conditions. The first approach was defined with default exchange coefficients from the phreeqc.dat database to identify and study the main parameters and coefficients that govern the model: cation exchange capacity, exchange coefficients, and activity coefficients. Then, these values were adjusted through iterative calibration until a good approximation between experimental and simulation breakthrough curves was achieved. This study proposes a suitable methodology and challenges for modeling the removal of metals from complex mine waters using synthetic ion exchange resins.