How to Shock, Flush, and Sanitize Your Home’s Plumbing System to Improve Water Quality

Over time, plumbing systems accumulate sediment, scale, and biofilm. These materials create ideal conditions for bacteria to grow. Shocking and sanitizing the system helps restore water quality, especially after contamination events, well disturbances, plumbing repairs, or long periods of disuse. The following procedure reflects the method commonly recommended by environmental health professionals and well maintenance specialists.

Step 1: Prepare the system for sanitizing

Turn off or bypass any water treatment devices that could be damaged by disinfectant. These include carbon filters, softeners, reverse osmosis units, and ultraviolet systems. Make sure you can access all faucets and fixtures throughout the home.

Step 2: Mix a potable-water-safe sanitizing solution

Use a chlorine-based disinfectant designed for wells and household plumbing. Follow established concentration guidelines. The solution should be strong enough to neutralize bacteria but not so concentrated that it damages plumbing components.

Step 3: Introduce the sanitizing solution into the plumbing system

Depending on your setup, the solution may be added through a well casing, pressure tank, or an approved injection point. Once added, allow the pump or municipal pressure to circulate the solution into the plumbing system.

Step 4: Open each faucet until disinfectant reaches it

Starting with the closest fixture to the supply source, open each faucet gradually. When you smell disinfectant in the water, close the faucet. Repeat this process at every sink, shower, tub, outdoor spigot, and low-use bathroom. This step ensures that the sanitizing solution reaches every part of the system.

Step 5: Allow sufficient contact time

Leave the disinfectant in the plumbing system for the recommended number of hours. Contact time is essential for breaking down biofilm and neutralizing bacteria. During this period, avoid using the water for drinking, cooking, or bathing.

Step 6: Flush the system thoroughly

After the contact time has passed, begin flushing the system. Open all faucets at once and let them run until the disinfectant odor disappears. This may take several minutes per fixture. Well systems may require pumping additional water to ensure all disinfectant is fully flushed out.

Step 7: Inspect the water for clarity and odor

Once flushing is complete, check that the water is clear and has no remaining disinfectant smell. If the water appears cloudy or yellow, or if an odor remains, continue flushing until the water returns to normal.

Step 8: Test the system to verify sanitization

Run a bacteria screening test, such as the test offered by DetektHome, to confirm that coliforms and E. coli are no longer present. Many environmental technicians recommend testing again after 48 to 72 hours to confirm that the system remains stable and no contamination returns.

Step 9: Restore all treatment devices

Reconnect or activate bypassed systems, including softeners and carbon filters, after the plumbing is fully flushed and test results show the water is safe. If any filters were exposed to disinfectant, they should be replaced.

Step 10: Establish a long-term maintenance plan

Homes with wells, older plumbing, hard water, or low-use fixtures often need periodic sanitizing. Testing water regularly helps determine when maintenance is needed. A screening tool makes it easy to monitor water safety and catch changes early.

Sanitizing the entire plumbing system is one of the most effective ways to eliminate bacterial growth and restore clean, reliable water throughout the home. When done properly, the procedure significantly reduces the risk of recurring contamination.

By A. Anagnos, Biomedical Engineering Specialist