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To study water quality problems associated with groundwater recharge, a tertiary treatment process, consisting of coagulation, sand filtration, and granular activated carbon (GAC) adsorption, was used in combination with a simulated soil aquifer treatment. The process significantly improved secondary effluent quality. GAC adsorption reduced organic substances expressed by UV-254, dissolved organic carbon as well as partially adsorbable organic halogens. The results of the Ames test show that the secondary effluent contains a high concentration of mutagens. GAC filtration removed adsorbable organic bromine slightly whereas GAC adsorption removed mutagens effectively. The simulated soil aquifer treatment was able to further reduce UV-254, dissolved organic carbon, and adsorbable organic halogens through biodegradation. Adsorbable organic bromine levels were also reduced by the soil aquifer treatment process. The given reclamation technology used for groundwater recharge is of benefit to the removal of dissolved organic carbon, UV-254, adsorbable organic halogens, and mutagenicity.