An innovative approach to remove mercury from Hg-rich ground-waters of the Abbadia San Salvatore Hg-mining area (Italy) using microcapsules containing trioctyl-methyl-ammonium-chloride (MC-TOMAC) is presented. Waters from three selected locations with mercury concentrations between 1.43 and 256.8 μg L−1 were studied. MC-TOMAC demonstrated high selectivity for mercury, being able to remove it entirely from ground waters in presence of relatively high concentrations of another anions in only one contact step. Besides, MC-TOMAC were able to satisfactorily remove the total mercury from ground waters when the mass ratio of mercury to MC-TOMAC was lower than 0.102 mgHg gMC-TOMAC−1 at pH 1, while up to 99.0 ± 2.0% of mercury was removed at natural pH. The relationship between the liquid and solid that can be treated in one contact step and a countercurrent contact in order to agree with the Council Directive 98/83/EC were stablished for one of the studied ground waters (S2). Additionally, a mathematical model based on the ideal mass action law in the solid phase and considering the metal speciation and their equilibriums in the liquid phase depending on the pH and chloride concentration was developed. Experimental extraction results were successfully fitted with the model, obtaining a value of the two unknown parameters, K{IE1} and K{IE2}, of 13622.5 and 2269.9 kg L−1; which represent the ion exchange equilibrium constants for the mercury uptake by MC-TOMAC for the species HgCl3-and HgCl42-, respectively. Besides, this model allowed to simulate the solid-liquid equilibrium curves at different pH values and chloride concentrations, indicating the suitable conditions to achieve the process.