Your Septic System After a Hurricane or Flood

After a hurricane or flood, use as little water as you can, stay out of floodwater, and do not have the septic tank pumped while the ground is still flooded or saturated. Wait until the water in the drain field soil has dropped, then have the system inspected if you see signs of damage. Safety comes first: sewage and floodwater can carry germs, septic tanks can hold dangerous gases, and electrical parts should stay off until they are dry.

This guide puts the official advice from the EPA, CDC, Florida Department of Health (DOH), UF/IFAS Extension, Florida DEP and FEMA into a simple before, during and after order. To check your flood zone and read about recent storms in our area, see flood zones and septic systems. If sewage is backing up right now, read sewage backing up into the house and call a septic company.

First, know what kind of system you have

UF/IFAS notes that conventional gravity-fed septic systems do not rely on electricity, so a power outage does not stop them. Mound systems, advanced treatment units and other systems that use pumps can be affected, and wastewater keeps collecting in the tank while the pump is off. Florida DOH says a system with any type of dosing pump, aerator or grinder pump will not work properly without electricity.

If you are not sure what you have, your permit records may say. Our county septic permit offices page lists who to ask. If you have an aerobic treatment unit, keep your maintenance company's number handy before storm season.

Before the storm

The CDC's flood guidance for septic owners lists these steps:

Seal the manhole and inspection ports to keep extra water out of the tank. If that means opening a tank lid, have your septic company do it.
Make sure the tank is at least half full. The CDC says this helps keep it from collapsing or floating. A storm is not the time to have it pumped empty.
Turn off the pump at the circuit box before the area floods, if your system uses electricity, and waterproof the electrical connections. Only switch a breaker if you can reach the panel without standing in water: the CDC says never to turn power on or off while standing in water. Leave the waterproofing to an electrician or your septic company. If you have an aerobic treatment unit, ask your maintenance company what it wants done before a storm.

If you plan to run a generator, the CDC warns that carbon monoxide is an odorless, colorless gas that can build up indoors and cause sudden illness and death. UF/IFAS recommends having a licensed electrician install the proper connection before hurricane season if a generator will run a well pump. Our flood resource adds UF/IFAS tips on cutting water use in the days before a storm and setting up a backup toilet.

During the storm and power outages

Use water as little as possible. Florida DOH says to "refrain from using water in your home as much as possible until the electricity is restored" if your system has a pump or aerator. The CDC suggests limiting toilet flushing, dishwashing, laundry and showers.
Stay out of floodwater. Florida DOH says not to enter floodwaters, since they may be contaminated. If you must, waders keep your body dry. It also warns that you and your pets can track contaminated material into the house or car.
Watch the drains. UF/IFAS lists slowly draining plumbing as a warning sign during an outage.

After the water goes down

Stay safe

Avoid contact with floodwater that may carry sewage. The CDC says to keep children and pets away from affected areas until cleanup is done.
Do not touch septic electrical devices until they are dry and clean (CDC), and have the connections checked for damage before restoring power (EPA).
Do not open or work inside the tank. The EPA says only trained specialists should clean or repair septic tanks, because they may contain dangerous gases. See septic tank safety.

Wait before using the system normally

The EPA advises not using the system until the water level in the drain field soil is lower than the water level around the house. Until then, UF/IFAS suggests skipping unnecessary laundry, dishwashing, bathing and toilet flushing. Do not drain floodwater from the house into a sink, toilet or other household drain (UF/IFAS).

Do not pump yet

Every agency we checked warns against pumping the tank out while the ground is waterlogged. Florida DOH: do not have the tank pumped, because "exceptionally high-water tables" can make the surrounding area cave into a tank that was pumped dry. The EPA: do not pump during flooded or saturated drain field conditions, because the tank can float out of the ground. The CDC: do not pump the tank out more than halfway, or it may float out of the ground. UF/IFAS: wait until floodwaters have receded and the soil is no longer saturated. Once the drain field is no longer flooded or saturated, the EPA says to have both the tank and any lift station pumped as soon as possible, to remove silt and debris that may have washed in.

Look for signs of damage

The CDC lists slow sinks and toilets, overflowing floor drains and sewage visible outside the home. The EPA adds settling or a system that cannot accept water. If you suspect damage, both say to have the system professionally inspected. Florida DOH says not to have the tank and drain field repaired until the floodwater has receded.

If you have a private well

Do not drink well water until you know it is safe (CDC). The EPA advises contacting your local health department about testing.

If sewage backed up into the house

Florida DOH says to keep everyone out of the affected areas. If the whole home was soaked, it advises leaving until carpets, rugs, drywall, baseboards and other affected areas have been thoroughly cleaned and disinfected or removed. If you clean up yourself, DOH says to wear protective clothing such as rubber boots and waterproof gloves, and the CDC adds goggles. The CDC also says to remove and discard drywall and insulation contaminated with sewage or floodwater. Our sewage backup guide covers the cleanup steps.

Temporary toilets and emergency orders

If using your plumbing creates a sanitary problem, Florida DOH suggests considering a rented portable waste receptacle. Florida's septic rule (Rule 62-6.0101(7)(a), F.A.C.) normally forbids using portable restrooms or portable holding tanks with permanent structures, but DEP has waived that after storms. After Hurricane Milton, for example, DEP's emergency final order of October 6, 2024 covered all 8 counties this site serves. It allowed portable restrooms, shower trailers and portable holding tanks where a septic system was damaged or not working because of the storm, for up to 120 days after the order ended. If a repair permit was issued within those 120 days, the temporary setup could stay until that permit expired.

The same order let contractors cover a newly installed but not yet inspected system with soil to protect it from the storm, as long as they told the county health department within 36 hours and uncovered it for inspection later. Each order applies to one storm, so check DEP's emergency order page for the current event, and ask your county health department before you set up a portable toilet.

Repairs, permits and contractors

Florida law requires a permit to repair, modify or replace a septic system, so most storm repairs usually need one. In most counties, you or your contractor apply to the county health department. In Marion County, DEP has issued septic permits directly since July 1, 2025. Florida's septic rule does not count pumping out the tank, where the drain field is not disturbed, as a repair (Rule 62-6.002), so it does not need a repair permit. Local rules can differ, so ask your county permit office. The Hurricane Milton order's septic section covered temporary toilets and covering new installations; it did not list a waiver of repair permits.

Before you hire anyone, check that the company is registered with DEP as a septic tank contractor. You can search DEP's public registration lookup, and our guide to verifying a Florida septic contractor walks you through it. Typical prices are in the septic cost calculator.

Paying for storm damage

FEMA. After Hurricanes Milton, Helene and Debby, FEMA said people who lost access to water through a private well or a damaged septic system "may be eligible for FEMA assistance." FEMA said it may reimburse the cost of a licensed technician's visit and estimate, and may pay for repair or replacement, costs that "typically are not covered by homeowner's insurance." Help depends on each disaster declaration. FEMA asks applicants to apply at DisasterAssistance.gov, in the FEMA App or at 800-621-3362, and to tell the FEMA inspector about septic damage. If the damage was not reported at the inspection, call the helpline to amend the application.

Insurance. Whether a policy pays depends on the policy, so ask your insurer or agent. For grants and loans, see septic repair assistance and financing.

Quick reference

When	Do	Do not
Before	Seal ports (lids opened by a professional), turn off the pump at the breaker before flooding if you can reach it without standing in water, keep the tank at least half full (CDC)	Have the tank pumped empty; touch a breaker while standing in water (CDC)
During	Use as little water as possible (DOH, CDC)	Wade in floodwater without protection (DOH)
Right after	Keep children and pets away, leave electrical parts off until dry (CDC)	Open or enter the tank (EPA), pump a saturated tank (DOH, EPA, UF/IFAS) or more than halfway (CDC)
Once the soil drains	Have the system inspected if you see damage; test well water (EPA, CDC)	Repair before the floodwater recedes (DOH)

Frequently asked questions

Can I flush the toilet during a hurricane?

Use water as little as possible. On a system with a pump or aerator, Florida DOH advises refraining from using water as much as possible until the power is back. While the drain field is flooded, the EPA says using the system less is the only way to prevent backups.

When can I use my septic system again after a flood?

The EPA says to wait until the water level in the drain field soil is lower than the water level around the house.

Should I have my tank pumped right after a hurricane?

No. Florida DOH, the EPA and UF/IFAS say not to have it pumped while the ground is still flooded or saturated, because the tank can float or the ground can cave in around it. The CDC says not to pump it out more than halfway.

Does FEMA pay for septic damage?

After the 2024 Florida hurricanes (Milton, Helene and Debby), FEMA said it may pay for a licensed technician's estimate and for repair or replacement of a storm-damaged septic system. Whether help is available depends on whether your area is in a declared disaster and on your application.

Will my aerobic unit work without power?

No. Florida DOH says systems with an aerator or pump will not work properly without electricity, so cut water use until power returns and then call your maintenance company if an alarm sounds or the system does not work normally once the power is back.