Methods and systems for treating cooling water of a retort are described. The methods and systems generate an aqueous ozone solution and combine the aqueous ozone solution with the cooling water. The methods and systems provide a safe, economical, easy to handle, and environmentally friendly solution for maintaining a retort cooling water system. The systems and methods herein remove contaminates from the cooling water, supply a continuous sanitizer created on-site, reduce the need for additional chemicals, and reduce the labor costs attributed to maintaining the retort cooling water system.