Who Issues Your Florida Septic Permit, by County

By the Marion County Septic Editorial Team Reviewed July 2026

Florida is part way through moving septic permitting from one state agency to another, so the answer to "who issues my septic permit" now depends on which county you are in. This page lists all 67 counties, names the agency for each, and gives the date it changed. It also flags where two state pages currently disagree, because that disagreement is sending homeowners to the wrong counter.

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The table

All 67 Florida counties. Of those, 17 are issued by FDEP and 48 by a county health department, while Gilchrist and Lafayette are not listed by FDEP at all. Every row comes from one source, FDEP's own permitting FAQ, read in full on 2026-08-02.

County	Permit issued by	FDEP since
Alachua	County health department	Not applicable
Baker	County health department	Not applicable
Bay	FDEP	2025-01-02
Bradford	County health department	Not applicable
Brevard	County health department	Not applicable
Broward	County health department	Not applicable
Calhoun	FDEP	2025-01-02
Charlotte	County health department	Not applicable
Citrus	County health department	Not applicable
Clay	County health department	Not applicable
Collier	County health department	Not applicable
Columbia	County health department	Not applicable
DeSoto	County health department	Not applicable
Dixie	County health department	Not applicable
Duval	County health department	Not applicable
Escambia	FDEP	2025-01-02
Flagler	County health department	Not applicable
Franklin	FDEP	2025-01-02
Gadsden	FDEP	2025-01-02
Gilchrist	Not listed by FDEP	Not applicable
Glades	County health department	Not applicable
Gulf	FDEP	2025-01-02
Hamilton	County health department	Not applicable
Hardee	County health department	Not applicable
Hendry	County health department	Not applicable
Hernando	County health department	Not applicable
Highlands	County health department	Not applicable
Hillsborough	County health department	Not applicable
Holmes	FDEP	2025-01-02
Indian River	County health department	Not applicable
Jackson	FDEP	2025-01-02
Jefferson	FDEP	2025-01-02
Lafayette	Not listed by FDEP	Not applicable
Lake	County health department	Not applicable
Lee	County health department	Not applicable
Leon	FDEP	2025-01-02
Levy	County health department	Not applicable
Liberty	FDEP	2025-01-02
Madison	County health department	Not applicable
Manatee	County health department	Not applicable
Marion	FDEP	2025-07-01
Martin	County health department	Not applicable
Miami-Dade	County health department	Not applicable
Monroe	County health department	Not applicable
Nassau	County health department	Not applicable
Okaloosa	FDEP	2025-01-02
Okeechobee	County health department	Not applicable
Orange	County health department	Not applicable
Osceola	County health department	Not applicable
Palm Beach	County health department	Not applicable
Pasco	County health department	Not applicable
Pinellas	County health department	Not applicable
Polk	County health department	Not applicable
Putnam	County health department	Not applicable
Santa Rosa	FDEP	2025-01-02
Sarasota	County health department	Not applicable
Seminole	County health department	Not applicable
St. Johns	County health department	Not applicable
St. Lucie	County health department	Not applicable
Sumter	County health department	Not applicable
Suwannee	County health department	Not applicable
Taylor	County health department	Not applicable
Union	County health department	Not applicable
Volusia	County health department	Not applicable
Wakulla	FDEP	2025-01-02
Walton	FDEP	2025-01-02
Washington	FDEP	2025-01-02

What changed, and why

The Clean Waterways Act of 2020 moved Florida's Onsite Sewage Program from the Department of Health to the Department of Environmental Protection, so that wastewater treatment and water quality sit under one agency. The move is happening in phases rather than all at once, and FDEP's own progress report says the remaining transfers depend on money being appropriated for them.

FDEP began issuing permits in 16 Northwest Florida counties, Escambia through Jefferson, on January 2, 2025. Marion County followed on July 1, 2025. FDEP's progress report notes that Marion County alone carries annual permit and inspection demand that rivals those first 16 counties together, which is why it moved on its own rather than inside a regional batch.

In FDEP counties, applications run through the FDEP OSTDS online portal or by mail to the program in Tallahassee. In county health department counties, the application goes to the local health department. The technical standards in Chapter 62-6, Florida Administrative Code do not change either way.

The two counties FDEP does not list

FDEP's permitting page says the transition of "the remaining 50 counties" depends on legislative approval, then names 48. Gilchrist and Lafayette appear nowhere on the page: not in the January 2025 group, not alongside Marion, and not in the county health department list.

Both are almost certainly county health department counties, because they are not in either FDEP group. That is an inference from a count, not something the page states, so this page marks them as not listed rather than quietly filing them under the health departments. If you own property in Gilchrist or Lafayette, confirm with the county health department before you apply.

What a permit costs

Fee ranges are set by Section 381.0066, Florida Statutes and apply statewide:

$25 to $125 for application review, permit issuance, or a system inspection.
$40 to $115 for a site evaluation.
$150 to $300 for an annual operating permit.

Those are the statutory outer limits, not the price. The exact amount inside each range is set by Rule 62-6.030, Florida Administrative Code in FDEP counties and by the county health department elsewhere, which is why two Florida property owners can pay different amounts for the same permit. Rule 62-6.030 was last amended effective June 8, 2026, so any figure published before that date may be out of date. Confirm the current amount with whichever agency issues your permit.

A permit fee is a small part of the project. What a system actually costs is driven by soil, water table, lot size, and whether springs rules require advanced treatment. Our drainfield replacement cost guide covers the Marion County ranges.

If you are in Marion County

Marion County moved to FDEP on July 1, 2025, so a new system, a full drainfield replacement, or a repair permit here goes through FDEP rather than the county health department. Our Marion County septic permit guide walks through the steps, the site evaluation, and the setback and sizing rules.

Marion County adds one thing most counties do not. Much of it sits inside the combined Silver and Rainbow Basin Management Action Plan, where new and replacement systems must be enhanced nutrient-reducing systems on any lot size, across the whole BMAP area rather than only a Priority Focus Area. That requirement follows the property, not the permitting agency. Our springs and BMAP guide explains where those rules apply and what they change.

How this page was built

Every county row on this page comes from one source, FDEP's Onsite Sewage FAQ, Permitting, read in full on 2026-08-02. The fee ranges come from the text of Section 381.0066, Florida Statutes, read the same day. Nothing here is assembled from news coverage or from other septic sites. Where a fact could not be verified at a primary source, this page says so rather than filling the gap: that is why Gilchrist and Lafayette carry their own status, and why no specific dollar amount is published for what FDEP charges inside the statutory ranges.

Permitting authority, fee rules, and county assignments change. Confirm anything you are about to rely on with the agency named for your county. If you find a row that is out of date, we would rather hear about it than leave it wrong.

Marion County Septic is an information and referral service. It connects property owners with independent licensed local septic contractors, and the contractor we send your request to pulls the permit and schedules the inspections.

Sources and where to verify

Ready to get a free quote from a licensed contractor?

Tell us about your project and get a free, no-obligation quote from a licensed local septic contractor.

Get a free quote Call (352) 605-0924

Your request goes straight to a licensed local septic contractor serving Marion County, usually within about an hour during the day, not a national lead list. Or call with your name, address, and what the job is: (352) 605-0924.

Frequently asked questions

Who issues septic permits in Florida?

It depends on the county. The Florida Department of Environmental Protection (FDEP) issues onsite sewage (OSTDS) permits in 17 counties: the 16 Northwest Florida counties that transferred on January 2, 2025, and Marion County, which transferred on July 1, 2025. In the rest of the state, permits are issued by the Environmental Public Health Program of the local county health department. The transfer of the remaining counties depends on legislative approval.

Why do two state websites give different answers?

The Florida Department of Health page listing which counties moved to FDEP names only the 16 Northwest Florida counties and tells everyone outside them to use their county health department. FDEP lists Marion County separately, with a July 1, 2025 date. A Marion County homeowner following the health department page would apply to the wrong agency. Both pages are linked in the sources below so you can check for yourself.

How much does a Florida septic permit cost?

Section 381.0066, Florida Statutes sets the ranges: not less than $25 and not more than $125 for application review, permit issuance, or a system inspection, and not less than $40 and not more than $115 for a site evaluation. An annual operating permit runs not less than $150 and not more than $300. The exact amount inside those ranges is set by rule in FDEP counties and by the county health department elsewhere, so confirm the current figure with whichever agency issues your permit.

Which counties does FDEP not list at all?

Gilchrist and Lafayette. FDEP's permitting page says 50 counties remain with county health departments but names 48, and those appear in none of its lists. By elimination they are county health department counties, but that is an inference rather than something the page states, so property owners there should confirm with the county health department before applying.

Does the permitting agency change what I have to build?

No. The technical standards live in Chapter 62-6, Florida Administrative Code and apply statewide, and springs Basin Management Action Plan rules apply based on where the property sits, not on who issues the permit. What changes is where the application goes, which forms and portal you use, and who inspects.

Updated August 2026