The secondary effluent from wastewater treatment plants was reused for industrial cooling water after pre-treatment with a laboratory-scale soil aquifer treatment (SAT) system. Up to a 95.3% removal efficiency for suspended solids (SS), 51.4% for chemical oxygen demand (COD), 32.1% for Cl− and 30.0% SO42− were observed for the recharged secondary effluent after the SAT operation, which is essential for controlling scaling and corrosion during the cooling process. As compared to the secondary effluent, the reuse of the 1.5 m depth SAT effluent decreased the corrosion by 75.0%, in addition to a 55.1% decline of the scales/biofouling formation (with a compacted structure). The experimental results can satisfy the Chinese criterion of Design Criterion of the Industrial Circulating Cooling Water Treatment (GB 50050-95), and was more efficient than tertiary effluent which coagulated with ferric chloride. In addition, chemical structure of the scales/biofouling obtained from the cooling system was analyzed.