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Striving for good IAQ in your facility means keeping an eye on a million little things, such as condensate drain lines. Condensate drain lines should be adequately trapped to overcome fan pressures and should be piped to drains on both rooftop and interior HVAC equipment.
If the static pressure of the fan on the air handling unit is greater than the depth of the trap and the condensate drain is on the negatively pressurized side of the air handling unit, air is pulled back through the drain trap. As the air enters the interior of the unit, it's like a little geyser of water from the drain line. Water from the drain line and the condensate pan could hit the interior insulation in the unit, and once that happens it becomes a likely site for microbial growth.
Condensate drain lines should not only be adequately trapped, but should be piped away from HVAC equipment to roof or floor drains. Condensate water that is not piped to drains can accumulate in low spots on the roof or in mechanical rooms. This water again becomes a breeding ground for microbes and could infiltrate the HVAC system through a rooftop outdoor air intake or a mechanical room that is acting as a mixing plenum for return and outdoor air.