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How to Prevent Algae in an AC Drain Line

Algae can grow in your AC’s condensation line, where moisture is always present. If left unchecked, it can cause a clog leading to water backing up and overflowing. Water damage to floors, walls, and ceilings can result. But did you know you can prevent algae from growing in an AC drain line? We’ll explain how so you can avoid HVAC damage, mold, and other potential consequences.

Empty the Drain Pan

During the warmer months, it’s a good idea to empty the drain pan. The longer water sits, the more opportunity algae has to grow. How often you manually empty the pan depends on whether you often notice standing water. To empty the drain line:

  • Turn off the power to your AC at the circuit breaker.
  • Open the air handler’s access door.
  • Locate the drain pan, which is usually below the evaporator coil.
  • Use a shop vac or towels to soak up the water.
  • Clean the drain pan with dish soap or vinegar.
  • Inset a thin wire brush into the drain pan to clean debris or remove potential clogs.
  • Locate the drain vent (T-shaped pipe), remove the PVC cap, and insert a wire brush to clean debris.

Remove Stubborn Clogs

If the condensate drain is clogged, run a plumber’s snake into the access point and down the pipe. Once you’ve broken through clogs or pulled out any debris, another option is to seal a shop vac or wet dry vacuum to the pipe with tape. This will make it easier for the vacuum to suck out any clogs. You can also thread a garden hose down the pipe vent, towards its exit, and turn on the water to flush out clogs.

The drain line can be unclogged from outside as well. To do so, locate the drain opening outdoors or near a floor drain. Clean around the pipe opening with a brush to remove leaves, bird’s nests, or other debris. A plumber’s snake, wet dry vacuum, shop vac hose, or garden hose can be used at this access point as well.

Clean the Drain Line

You can try these methods for cleaning AC drain lines:

  • Vinegar: At the pipe vent access point, pour a cup of white distilled vinegar. The vinegar will kill any algae along with bacteria and mold in the drain line. Let the vinegar sit for a few hours and then pour water in to flush out the line. Have someone check whether the line is draining. If it drains, the clog is gone, and you can put the PVC cap back on the vent, reattach the panel, and turn the AC breaker back on.
  • Algae Pan Strips/Tablets: Place the strips or tablets in the drain pan and replace twice a year. These treat the water before it drains into the condensation line, so algae cannot grow. If you have an open-line system without a drain pan, place the tablets into the line and replace them every six months. You can pour a cup of bleach into the condensation line’s access point as well (once a year or biannually if you notice algae growth). There are also liquid additives formulated to prevent algae growth (add every 90 days when the system is in use).
  • Bleach, Vinegar, or Algaecide: While some ACs automatically shut down in case of a blockage, others may require a cleaning once or twice during the cooling season. Pour one of these options into the access line of the indoor unit and wait 30 minutes. Then use water to flush the line. If water stays in the drain pan there is probably a blockage. You can loosen small blockages with surgical tubing. But if that doesn’t help, shut the system off and use a wet-vac, or call a technician for help.

Call Air Pros for Help

If you have a clog or algae in an AC drain line, our technicians are trained and equipped to quickly deal with the problem. The condensation pan and drain line are important points of AC maintenance. During any maintenance visit, our team will thoroughly inspect the indoor and outdoor components of your HVAC system and provide any adjustments or fixes needed. One-, two-, and three-year HVAC service plans are available. To learn more or schedule service 24/7, call 844-629-1691.


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