A method for controlled removal of carbonate blockage from interior walls of water conduit systems having substantial reduction in flow capacity. A section of the system to be cleaned is isolated and an aqueous liquid is circulated to establish baseline liquid flow rates. An acidic cleaning composition which removes the blockage but which generates carbon dioxide gas is then added under controlled conditions to a circulating aqueous cleaning solution. The fluid flow rates and pH are monitored throughout treatment. Adjustments are made if necessary to maintain a controlled amount of carbon dioxide gas liberated. The aqueous acid cleaning solution is circulated in an open loop system with continued addition of acid until the outflow rate decreases and once again equals the inflow rate. Substantial inorganic carbonate deposits are thus removed from water conduit systems while dangerous conditions due to excessive generation of carbon dioxide gas are avoided.