Chlorine for Legionella and Waterborne Pathogen Control and Secondary Disinfection

How does chlorine work to kill Legionella?

Chlorine (CL2) kills Legionella and other pathogens by breaking down the bonds in the molecules. It is a widely used disinfectant due to its effectiveness and relatively low cost. Since CL2 is one of the most reactive elements, it easily reacts with other elements. It does this by breaking down the chemical bonds in the enzymes of Legionella. When chlorine contacts these enzymes, one or more of the hydrogen atoms in the enzymes are replaced by chlorine. This change in molecular structure causes the enzyme to fall apart or change shape, which is what kills Legionella. Chlorine is considered a secondary disinfection method.


Watch our video comparison of secondary disinfection approaches.

Importantly, while chlorine is accessible and inexpensive, it doesn’t do a good job of penetrating biofilm. Chlorine Dioxide, Mixed Oxidant Solution (MOS – MIOX), and Advanced Oxidation Process (AOP) are better suited for removing biofilm and preventing it from forming. See the chart below to see how chlorine levels affect biofilm.

Free Chlorine Levels Effects on Biofilm

Free chlorine versus pH for Legionella control

Free chlorine versus pH for Legionella control

Chlorine applications and Legionella control

Chlorine can be used as a primary or secondary disinfectant to control Legionella and pathogens. It is commonly seen in water purification, swimming pool maintenance, and wastewater. It is popular because it is relatively easily applied/injected, easily measured, and cost-effective. Chlorine can also be used as an oxidizer in iron filters; it will both oxidize and precipitate the iron from the water while also acting as a disinfectant.

How to size a Legionella control chlorine system

Legionella chlorine injection systems are sized based on water quality, gallons used per day, peak water usage, and desired residual. Use our sizing calculator today.

Do You Need Legionella Testing?

Legionella testing can help determine whether bacteria are present and help verify whether remediation or an ongoing secondary disinfection program is working effectively. Testing may be appropriate to establish a baseline, after remediation, or as part of a water management program.

Learn more about Legionella testing, review Legionella testing prices, or contact Legionella Control Systems.

Legionella control chlorine water system service

Need more information on Legionella control? Contact Legionella Control Systems at [email protected] or 888-416-8626 for design, service, and sales of Legionella control water systems in Indiana, the Midwest, and throughout the U.S. Our experienced engineers are ready to help.


Contact Legionella Control Systems for CDC Legionella risk assessment and Legionella testing.

By Chris Nancrede. Last Updated: July 28, 2026