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Fall/Winter Cooling Tower Shutdown: Why Cleaning is Critical and How to Stay Compliant

  • The NuChem Crew
  • Sep 12
  • 9 min read

Updated: 14 hours ago

NYC winter cooling tower shutdown

As the cooling season winds down and temperatures drop, building owners and facility managers need to prepare their cooling towers for fall and winter. Properly shutting down a cooling tower is not as simple as flipping a switch, it requires careful cleaning, disinfection, and compliance with regulations. In this post, we’ll explain why it’s so important to clean your cooling tower before shutting it down, outline best practices for a fall/winter shutdown, discuss NYC/NYS cooling tower regulations, and show how NuChem Corp can help ensure a smooth transition into the off-season.


Why Cleaning Your Cooling Tower Before Shutdown Is Essential


Preventing Health Hazards: The primary reason to thoroughly clean and disinfect a cooling tower prior to shutdown is to prevent the growth of Legionella and other harmful bacteria. When a cooling tower is idle, stagnant water and residual biofilms create a perfect breeding ground for Legionella, the bacteria that causes Legionnaires’ disease. The last thing any building owner wants is a Legionella outbreak traced back to an improperly maintained tower. By cleaning and sanitizing all interior surfaces at shutdown, you remove biofilm, algae, and sediment that could harbor bacteria over the winter. This proactive step keeps your building occupants safe and eliminates health risks when the system is started up again in spring.

Maintaining Equipment Efficiency: Neglecting to clean a cooling tower can lead to a host of mechanical and efficiency problems. Over a cooling season, mineral scale, dirt, mud, and debris accumulate on tower surfaces and in the basin. If not removed, this gunk can harden or corrode surfaces during the off-season and cause blockages in fill media and tubing. When cooling is needed again, a dirty tower will have reduced heat transfer efficiency and may put strain on chillers and pumps. In fact, scale buildup forces the system to work harder and can drive up energy consumption and operating costs. By performing a deep cleaning before shutdown, you help preserve the tower’s performance, extend its lifespan, and avoid costly repairs or inefficiencies caused by fouling.

Easier Spring Start-Up: A tower that has been cleaned and serviced in the fall will be much easier to bring back online when warm weather returns. You won’t be faced with foul odors, clogged strainers, or heavy biofilm deposits at startup because those issues were addressed before winter. This means a smoother start-up process with less downtime and it’s also a requirement in many cases. NYC regulations actually mandate that any cooling tower idle more than 5 days must be cleaned and disinfected before restart.


Best Practices for Fall/Winter Cooling Tower Shutdown


Below are key best practices and steps to ensure your cooling tower is safely taken out of service for the season:


  1. Plan and Schedule the Shutdown: Coordinate with your facility team or HVAC service provider to choose the right time for shutdown, ideally when cooling is no longer needed. Give yourself enough lead time before freezing weather. Planning ensures that qualified personnel and any necessary chemicals or equipment (for cleaning/disinfection) are ready on shutdown day.

  2. Drain and Flush the System: Begin by completely draining the cooling tower’s water from the basin and system piping. Open the tower drain and let the water flow out. It’s important to flush the cold water basin to wash out sediment and sludge; do this with the strainer screens in place to catch debris. Removing all water and dirt now prevents standing water from freezing or becoming stagnant over winter. Many experts recommend leaving the drain valve open once empty, so rain or meltwater cannot accumulate in the basin.

  3. Thoroughly Clean Surfaces and Components: Once drained, perform a deep cleaning of the cooling tower’s interior. Physically remove any scale, algae, and dirt from the basin, fill media, drift eliminators, and splash bars. This may involve pressure washing and vacuuming the basin and other surfaces, and scrubbing or replacing fill if heavily fouled. Pay special attention to components like nozzles and the distribution arms/spray tree, ensure they are clear of deposits. All slime, biological growth and scale deposits should be removed during this cleaning phase.

  4. Disinfect the Tower: After mechanical cleaning, the tower should be chemically disinfected to kill any remaining bacteria. This typically involves adding an EPA-registered biocide or chlorine (hyperhalogenation) to water in the basin and circulating it through all tower parts for a prescribed time (often 6 to 24 hours), then draining the solution. Disinfection is critical for Legionella control and is required by regulations in NYC and NYS. The rule call for tower disinfection at least twice per year (before startup and after shutdown). Be sure to follow all safety guidelines when handling chemicals, or hire a water treatment professional to perform the disinfection properly.

  5. Clean and Service Mechanical Components: With the tower offline, take the opportunity to perform preventive maintenance on fans, pumps, and other mechanical parts. Clean out strainers and screens and reinstall them, inspect and clean the drift eliminators and louvers, and wipe down fan blades. Lubricate bearings on the fan motor and check belt drives for proper tension (replace or adjust belts if needed). Also inspect metal surfaces and the tower structure for any corrosion or damage. You may choose to touch up paint or coatings now (“clean and refinish as required” is a common step). Addressing mechanical issues during the shutdown will ensure the tower is ready to run reliably next year.

  6. Shut Off and Winterize Water Lines: Close the make-up water supply valve to the tower to prevent any water from entering while it’s offline. Drain all piping connected to the cooling tower, including make-up lines, distribution pipes, and condenser water lines that could be exposed to freezing temperatures. Any trapped water in these lines can freeze and cause pipe bursts, so use low-point drains or compressed air to blow out remaining water. Also, consider protecting components like coils or exchangers if they will remain in place some systems have built-in heaters (e.g. basin heaters or motor space heaters) that should be energized to prevent freeze damage. Ensure the tower and its connected systems are fully winterized against freezing.

  7. Documentation and Compliance: After cleaning and shutdown, document all the steps taken. It’s a best practice to have a cooling tower maintenance log where you record the date of cleaning, disinfection, inspections, and any repairs. In New York City, you should obtain a Certificate of Cleaning and Disinfection from your water treatment provider for each service, and keep these on file to show inspectors. Make note of the seasonal shutdown date, in New York State’s cooling tower online registry, seasonal towers require you to input the shutdown date (and later the startup date) each year. Good recordkeeping now will simplify your regulatory reporting and annual certification (due by Nov 1 in NYC) later on.


By following these best practices, you’ll ensure your cooling tower is safely shutdown for the winter. A clean, dry, and well-maintained tower will stay in good condition during its downtime and be ready for trouble-free reactivation when the weather warms up.


NYC/NYS Cooling Tower Regulations for Seasonal Shutdowns


New York has some of the nation’s strictest cooling tower regulations, which were established to prevent Legionella outbreaks. Building owners in NYC and NYS must adhere to maintenance and reporting rules year-round, including specific requirements related to seasonal shutdowns. Here are a few key compliance points to keep in mind:


  • Biannual Cleaning/Disinfection: Both NYC and NYS regulations require that cooling towers be cleaned and disinfected at least twice a year – typically once before the cooling season begins and once after it ends. If your tower runs year-round, you still need at least two cleanings annually. This means that a thorough cleaning and biocide treatment at fall shutdown isn’t just good practice, it’s the law in NYC/NYS.

  • Seasonal Shutdown Procedures: If your cooling tower is operated seasonally (for example, only running in spring and summer), state rules mandate that you safely disinfect and shut it down at the end of the season, and later clean and disinfect it before the next startup. You are also required to update the New York State cooling tower registry with the date of your shutdown and subsequent startup as part of your 90-day compliance reporting cycle. NYC’s Health Department similarly emphasizes that when a system is shut down, it must be completely drained and protected from contamination while offline. Any water remaining in the system counts as “partial operation” and would necessitate ongoing treatment or a proper startup procedure if the tower is to run again.

  • Pre-Startup Requirements: Before a cooling tower is restarted after a long idle period, regulations kick in to ensure safety. NYC law requires an owner to clean and disinfect a tower that has been shut down for more than five days before startup (and do so no more than 15 days prior to the startup). A Legionella culture test must also be taken shortly after reactivation in such cases. In practice, this means you should never plan to simply refill and run a tower in spring if it wasn’t properly cleaned at shutdown – you’ll need to perform a full cleaning and disinfection first. Doing it at shutdown sets you up for compliance when restarting.

  • Annual Certification and Recordkeeping: NYC requires building owners to submit an Annual Certification by November 1 each year, affirming that each cooling tower under your care was inspected, tested, cleaned, and maintained in accordance with the law. Failing to file this certification can lead to fines up to $10,000 for late or missing reports. Additionally, all inspection reports, cleaning/disinfection logs, and water testing results should be documented in your Maintenance Program and Plan (MPP). Both city and state inspectors can audit your records at any time to verify that you performed the required shutdown cleaning and other tasks. Non-compliance can result in significant penalties, and more importantly, it endangers public health.


Staying on top of these regulations may seem daunting, but they essentially codify the best practices that keep your cooling tower safe. By planning your fall shutdown with compliance in mind, performing the required cleaning/disinfection and filing the proper notices, you’ll meet your legal obligations and greatly reduce the risk of issues like Legionella in your building.


How NuChem Corp Can Help Ensure a Smooth Shutdown


Preparing and executing a proper cooling tower shutdown can be a complex task, but you don’t have to do it alone. NuChem Corp is a full-service water treatment company with expertise in cooling tower maintenance and Legionella compliance. We partner with building owners and facility managers to take the hassle out of seasonal transitions. Here are some ways NuChem Corp can help with your fall/winter cooling tower shutdown:


  • Professional Cleaning & Disinfection: Our team of trained water treatment specialists will perform a comprehensive cleaning and disinfection of your cooling tower at the end of the season. We remove biological growth, scale, and debris from your tower’s basin, fill, and piping, then apply effective biocidal treatments to sanitize the system. We follow industry best practices and NYC/NYS guidelines to ensure your tower is left clean, drained, and safe for the winter shutdown.

  • Compliance with NYC/NYS Regulations: NuChem Corp stays up-to-date on all cooling tower regulations and will help keep you compliant. We make sure that the required twice-annual cleanings (pre-startup and post-shutdown) are completed and properly documented. Our staff can assist in updating your state cooling tower registry with seasonal shutdown information, and we’ll provide you with the cleaning certificates and service reports you need for your records. When it’s time for annual certification, you’ll have peace of mind knowing every maintenance task has been done in accordance with NYC Health Department rules.

  • Preventative Maintenance & Repairs: In addition to water treatment, we can inspect your cooling tower’s mechanical components during the shutdown process. Our technicians will check strainers, fans, pumps, and controls, lubricating and servicing parts as needed. If we find any issues (for example, a worn-out belt or a corroded section of fill), we can address them during the winter downtime. This proactive maintenance means your cooling tower will be in optimal condition and ready to perform when you restart it in the spring.

  • Expert Guidance and Scheduling: Unsure about the right timing or procedure for shutdown? NuChem Corp provides expert guidance. We work with your team to schedule the shutdown at the ideal time and ensure all necessary steps are covered. Our professionals bring years of experience managing cooling tower off-season layups, so we can anticipate challenges like sudden cold snaps or tricky drain setups. By letting us handle the shutdown process, you can focus on other facility needs while we take care of protecting your cooling system.


A fall/winter cooling tower shutdown is a critical part of your facility’s maintenance cycle. By cleaning and disinfecting the tower before shutting it down, you safeguard against health risks like Legionella, preserve your equipment’s integrity, and comply with stringent NYC/NYS regulations. Following best practices, from draining and cleaning to thorough documentation, will set your cooling tower up for success when cooling season comes around again. And remember, you don’t have to navigate this process alone. NuChem Corp is here to help with professional water treatment services and compliance expertise, so your building can enjoy a smooth transition into the winter and a trouble-free startup in the spring. With the right approach and support, you can shut down your cooling tower confidently, knowing your building and its occupants are protected.


At NuChem Corp, our goal is to make your cooling tower management safe, compliant, and worry-free. With our help, you can transition into the fall and winter seasons confidently, knowing that your cooling tower has been properly cleaned, maintained, and secured against hazards. When the warm weather returns, we’ll also be there to assist with startup, ensuring water quality is excellent and your system starts up smoothly.



Content on the NuChem Corp Blog is for informational purposes only and does not replace professional advice. External sites linked are provided for convenience; NuChem Corp is not responsible for their accuracy or content.



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