Quick Answer: Flushing pipes helps get rid of bacteria floating in the water, but it doesn’t do much for the tough stuff, like biofilm, that sticks to pipe walls. Chlorination can keep those free-floating bacteria in check, but it won’t fully clear out established biofilms. When you combine flushing with chlorination, you’ll see a bigger drop in microbes than with either method alone. Just remember, biofilms can grow back pretty quickly, often within days after treatment stops.