In the cooling water system (CWS), being infrastructure for large research facility, one of the important issues is the operation reliability, and then the minimizing of operation and maintenance costs. For optimum design, we studied the cooling loops for pulse and continuous operations of clients, volume and inside piping structure of storage tanks, two-step heat exchanger, safety devices and energy conservational operation of the CWS. During commissioning, the flow rate shortage due to increase of pump head by rise of client pressure drop was resolved as the operation of a stand by pump. The unexpected water pressure hunting occurred at an ion cyclotron ranges of frequency (ICRF) inlet port was stabilized by exchange of the starting system of motor and transfer of a constant flow rate valve from the water outlet port to the inlet port of the ICRF. We confirm that a polishing system, a first neutral beam injection cooling loop and a plasma facing component baking system can be stably operated in the upgrade step of clients. To improve the coefficient of performance and stability of operation in chiller, we will develop the new header, decreasing the gap of inlet temperature of cooling towers.