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In a significant flood, elements of or all of the HVAC system may be submerged in the flood waters. Even in components that were not submerged, such as air ducts, moisture can collect inside them due to how saturated the air is inside the facility.
Once the water has receded and if the system is deemed salvageable, it is important to thoroughly clean the components to ensure microbial contamination, dust and debris do not damage the facility's indoor air quality. All components of the HVAC system will need to be inspected, cleaned, and disinfected by a qualified professional.
Here are some tips from the Center for Disease Control on remediating flooded HVAC systems.
If unaffected parts of the building will remain in use during remediation, seal off the affected area with vapor-retarding barriers and maintain negative pressure in the affected area by using blowers to ventilate the area.
Any material that absorbed liquid will need to be removed, including insulation and filter media. When cleaning out the system, pay special attention to filter racks, drain pans, bends and horizontal sections of air ducts.
Disinfect the system's surfaces with a bleach solution and follow with a clean water rinse. Work from clean-to-dirty to avoid recontaminating areas just cleaned. If a component cannot be adequately cleaned and disinfected, it should be replaced.
Before reoccupying the space, run the HVAC system continuously at normal temperatures for two or three days to flush out the air. If after this point, there are still odors, investigate and remediate any overlooked areas of the system. Be sure to replace the air filters used during the remediation before normal occupancy resumes.
For more, go to the CDC at http://www.cdc.gov/niosh/topics/emres/Cleaning-Flood-HVAC.html