The best time to sanitize your reverse osmosis system is when you change your filters. According to US Water Systems, you will first need to shut off the water running to your reverse osmosis system, then open the faucet to depressurize the system, and remove all filters and the membrane. You will then need to pour a sanitation packet into the first filter's housing and turn the water supply back on so it can run through the system. After the tank is full, you should turn the water back off and run the faucet to drain the system. Repeat this process twice to make sure all the sanitizer has been flushed out.