Yes, that is exactly right, and that's why large wastewater tanks in industrial settings hae circulating pumps. Unfortunately, the bacteria are one step ahead; they form biofilms--dense, sometimes crusty hard films that create favorable microenvironments. So once a biofilm forms, even if you circulate a disinfectant, the outside of the film will be killed, but the inside is still cozy for the organisms to live, and they come back. It's a huge engineering task to create water systems with no dead legs or even small pockets of low circulation so that the films can't get a hold to begin with.