Who Regulates Septic Systems in Florida Now? (DEP and County Health Departments)

The Florida Department of Environmental Protection (DEP) has run the state's septic program since July 1, 2021. But in most counties you still deal with the county health department, which takes applications and issues permits on DEP's behalf. Marion County (Ocala) is the main exception in Central Florida: DEP has issued septic permits there directly since July 1, 2025.

So the short version is: DEP writes and enforces the rules, and your county health department is usually the office you call. This guide explains how that split came about, which office handles which job, and where cities, sewer utilities and the federal government fit in. Florida has an estimated 2.6 million septic systems, used by about 30% of residents, according to DEP, so these offices handle a lot of work.

How the program moved from the Department of Health to DEP

For decades, Florida's septic program sat with the Department of Health (DOH). The move to DEP started in the 2020 legislative session with Senate Bill 712, which the Pasco County health department calls the Clean Waterways Act. Governor DeSantis signed it on June 30, 2020, as Chapter 2020-150, Laws of Florida. DEP took over the program on July 1, 2021.

In 2021 the two agencies signed an interagency agreement, under which the program began operating on July 1, 2021. The model recommended in the agencies' 2020 transfer report ("scenario B") kept the septic staff in county health departments as DOH employees, with their work on the program under DEP's direction from July 1, 2021. The state law that covers septic systems, section 381.0065 of the Florida Statutes, now defines "department" as DEP.

The rules moved too. The statewide septic standards are now Chapter 62-6 of the Florida Administrative Code, "Standards for Onsite Sewage Treatment and Disposal Systems". They used to be numbered 64E-6, and you will still see "formerly 64E-6" in the history notes of each rule. The state calls septic systems onsite sewage treatment and disposal systems, or OSTDS, so that is the term you will see on forms and agency pages.

Which counties DEP permits directly

DEP has started taking over permitting and inspections itself, county by county. According to its permitting FAQ:

Phase 1, the Panhandle: 16 counties from Escambia east to Jefferson moved to DEP on January 2, 2025.
Marion County: moved to DEP on July 1, 2025. This includes Ocala and Belleview.
All other counties: DEP says the dates are "to be determined depending on legislative approval".

That leaves 7 of the 8 counties this site covers with their county health department: Hillsborough, Pinellas, Pasco, Orange, Osceola, Seminole and Lake. If you live in Tampa, St. Petersburg, Orlando, Kissimmee and Sanford, for example, you apply at the county health department. In Marion County you apply to DEP, through its online portal at ostds.floridadep.gov or by mail. Our county septic permit offices page lists each office with its phone, address and how it takes applications.

Who to call for what

Here is where each common septic question goes. "Your permit office" means the county health department, or DEP in Marion County.

What you need	Who handles it
A permit for a new system, repair, modification or abandonment	Your permit office
Old permits, site plans and inspection records for your property	Your permit office. Some counties put records online; Hillsborough uses a system called e-Bridge.
An operating permit for an aerobic treatment unit (ATU) or a commercial system	Your permit office
Sewage on the ground, a failing system next door, or another septic health hazard	Your permit office (see "Complaints" below)
Checking a septic contractor's registration	DEP, on its public online searches
Reporting someone doing septic work without a registration	DEP's reporting page sends you to the county health department
Whether your lot is in a springs or nitrogen-reducing area	DEP sets the rules and publishes the maps and tables; your permit office can tell you how they apply to your lot
Sewer availability, connection fees and septic-to-sewer projects	Your sewer utility (a city, county or private utility)
Testing private well water	The EPA suggests checking with your local health department

Permits and inspections

State law says no one may construct, repair, modify, abandon or operate a septic system "without first obtaining a permit approved by the department" (s. 381.0065(4), F.S.). The county health department, or DEP in Marion, takes the application, reviews the site evaluation, issues the permit and inspects the work. The Hillsborough County health department's septic page, for example, lists construction permitting and inspection, operating permits and inspections for ATUs and commercial systems, and pump truck permitting among its services.

Florida's septic rule does not count routine pumping, where the drain field is not disturbed, as a repair (Rule 62-6.002), so it does not need a repair permit. Nor do a few other small jobs. Local rules can differ, so ask your county permit office. Our list of county septic permit offices shows who to ask.

Complaints about a failing system

State law gives DEP the job of enforcing Florida's sanitary nuisance law for "nuisances involving improperly built or maintained septic tanks or other onsite sewage treatment and disposal systems" (s. 381.0065(3), F.S.). In practice, DEP sends people to the county health department. Its page on reporting unlawful septic contracting, for example, says: "Please contact the local county health department so they can assist you further with the complaint."

Hillsborough's health department, for example, takes public health complaints by phone and through an online form. Its complaints page says complaints within its jurisdiction "are recorded and investigated", and that it follows up when there is a sanitary nuisance or a potential health hazard. If you live in Marion County, where DEP now handles septic permits, ask DEP's Onsite Sewage Program where to send a septic complaint.

Contractors

Septic tank contractors are registered by DEP under Part III of Chapter 489, Florida Statutes, through its Operator Certification Program. This did not change county by county: one statewide register covers everyone. You can check a registration on DEP's public search. Licensed plumbing contractors are licensed separately, by the Construction Industry Licensing Board at the Department of Business and Professional Regulation (DBPR). Our guide on how to check a Florida septic contractor's registration walks through the searches and what a result means.

Aerobic treatment units

An aerobic treatment unit has two extra layers of oversight. The owner needs an operating permit, valid for 2 years, from the permit office. The owner also needs a service contract with a maintenance entity permitted by the department, which inspects the unit at least twice a year. (The owner of an owner-occupied single-family home can instead be permitted to maintain the unit after training certified by the manufacturer's representative.) The law also says buildings that use an ATU "shall be inspected by the department at least annually."

Where DEP sets the rules directly

Even in counties where the health department issues the permit, some decisions come straight from DEP:

Springs and nitrogen rules. Since July 1, 2023, new systems on lots of 1 acre or less in DEP's basin management action plan (BMAP) areas must be nitrogen-reducing where sewer is not available. Some springs plans go further. In the Silver/Rainbow springs plan, which lies largely within Marion County, DEP's August 2026 table lists the upgrade for repairs on any size lot. DEP publishes these tables and maps. See our guide to nitrogen-reducing septic systems.
The standards themselves. Setbacks, drain field sizing, tank rules and fees are all in Chapter 62-6. The fact-checked summaries are on our Florida septic regulations page.
Contractor registration and discipline. DEP registers contractors, approves their continuing education and can act against a registration.

Local rules can add to the state ones. DEP's FAQ notes that "many counties have local ordinances that may exceed state requirements for OSTDS." Your permit office can tell you whether any apply to your lot.

Where cities and sewer utilities fit in

In the 8 counties we cover, cities do not issue septic permits. None of the county pages we checked say city limits change who issues them: the county health department, or DEP in Marion, covers the whole county.

Cities and counties matter in a different way when they run the sewer. State law requires a home on septic to connect to a "publicly owned or investor-owned sewerage system" within 365 days of written notice that sewer is available (s. 381.00655, F.S.). The notice comes from the owner of the sewer system. The permit office still handles the septic side, because abandoning the old tank needs a permit. Our septic vs. sewer guide covers the connection law and local septic-to-sewer programs.

What the federal government does (and doesn't)

The U.S. Environmental Protection Agency (EPA) publishes guidance for septic owners, and this site uses it often. But the EPA says it "does not regulate single family home septic systems." Individual systems are regulated by states, tribes and local governments. In Florida, that means DEP and the county health departments.

How to find your office in 3 steps

Find your county. Septic permits follow the county, not the city or ZIP code.
If you are in Marion County, go to DEP. Anywhere else in the 8 counties we cover, go to the county health department's environmental health office.
Use the county septic resource finder or the permit offices list for the phone number, address and how to apply.

If you need work done, the company you hire usually prepares and files the permit paperwork. Ask who will apply and whose name will be on the permit. You can browse septic companies in the directory.

Frequently asked questions

Does the Florida Department of Health still handle septic systems?

Partly. DEP has been responsible for the program since July 1, 2021, but in most counties the county health department (part of DOH) still takes applications, issues permits and inspects systems on DEP's behalf. Marion County and the 16 Panhandle counties are handled by DEP directly.

Who do I call about a septic permit in Ocala?

Florida DEP. Since July 1, 2025, DEP has issued septic permits in all of Marion County, and applications go through its online portal or by mail. The Marion County health department no longer issues them. The permit offices page has the contact details.

Will my county switch to DEP permitting soon?

DEP has not set a date. Its FAQ says the timing for the remaining counties is "to be determined depending on legislative approval". Check your county health department's septic page before you apply.

Is "64E-6" still the rule?

No. The same standards are now Chapter 62-6, F.A.C. Older documents and contracts may still cite 64E-6.

Who do I report an unregistered septic contractor to?

DEP's page for reporting unlawful septic contracting asks you to contact your local county health department, which can help with the complaint.

This guide is general information, not legal advice. Your permit office has the final word on your property.