Septic and well permitting in Northeast Florida

Who regulates septic systems in Florida

Onsite sewage treatment used to sit with the Florida Department of Health. Responsibility transferred to the Department of Environmental Protection on 1 July 2021. That was the transfer of oversight — of enforcing the state laws and rules. Day-to-day permitting moved separately, and later.

DEP began issuing permits itself on 2 January 2025 in sixteen Northwest Florida counties, running from Escambia east to Jefferson, and added Marion County on 1 July 2025. Everywhere else, including here, the county health department still issues the permit and still holds the records.

DEP has not published a schedule for the remaining counties — its own material ties further transitions to legislative approval. Anyone who gives you a firm date for Duval, Clay, Nassau or St. Johns is guessing.

Who issues your septic permit, county by county

Duval, Clay, Nassau, St. Johns and Putnam have not transitioned. Septic permitting in all five still runs through the county health department, which is also who holds the records on your existing system.

This matters more than it sounds. A permit is not paperwork you file after the fact — on new installations and on most drain field replacements, the permit has to be in hand before work starts, and it follows a site evaluation. That sequence is what sets the real timeline on a job.

How much room a system needs on your lot

Whether a lot can take a septic system is mostly a question of distance. Rule 62-6.005 of the Florida Administrative Code sets the minimum separations. It is a Department of Environmental Protection rule. The version now in force took effect on 8 June 2026. These are minimum distances, so a system cannot sit closer to a listed feature than the rule allows.

The list below gives the separation distances Rule 62-6.005 sets out in subsections (1), (2), (3) and (8). Those subsections cover a little more than distances. Subsection (2) also deals with tank lids under a driveway and with backflow devices on irrigation lines. Subsection (8) covers effluent transmission lines made of schedule 40 PVC. For that pipe, its distances override the rest of the rule. Each distance below runs from the septic system to the feature named.

• 75 feet to a private potable well, or to a multi-family water well. Rule 62-6.002 defines both terms
• 100 feet to a public drinking water well. That figure applies where the facility the well serves has an estimated sewage flow of 2,000 gallons a day or less
• 200 feet to a public drinking water well, where that flow is more than 2,000 gallons a day
• 50 feet to a non-potable water well
• 10 feet to any storm sewer pipe, to the maximum extent possible. In every instance the setback must not be less than 5 feet
• 15 feet to the design high-water line of retention areas, detention areas and swales. That covers areas designed to hold standing or flowing water for less than 72 hours after rain. The same 15 feet applies to the design high-water level of normally dry drainage ditches and normally dry individual-lot stormwater retention areas. Rule 62-6.005 sets this separation in subsection (1) and again in subsection (3)
• 75 feet, measured laterally, to the boundaries of surface water bodies, except as sections 381.0065(4)(g)1. and 2. of the Florida Statutes provide. This is a separate rule from the 75 feet to a private potable well
• No part of the system may sit under a building, or within 5 feet of building foundations, mobile home walls or swimming pool walls. Foundations include the pilings under an elevated house
• The system must stay 5 feet from a property line. That 5 feet does not apply where the line abuts a utility easement holding no underground utilities. It also does not apply where a recorded easement provides for a system serving more than one lot or owner
• Sidewalks, decks and patios are not subject to that 5-foot setback, but a drain field must not be installed beneath them
• 10 feet to water storage tanks that sit in contact with the ground, and to potable water lines. A potable water line is exempt if it is sealed inside a sleeve for at least 10 feet from the nearest part of the system. It is also exempt if it is schedule 40 PVC or stronger
• A water line must not run within 24 inches of the system. A potable water line within 5 feet of the drain field must not sit lower than the drain field absorption surface
• 15 feet to groundwater interceptor drains
• A schedule 40 PVC effluent transmission line is treated on its own. It must be at least 25 feet from private potable wells, irrigation wells and surface water bodies when installed. It must be at least 2 feet from property lines and building foundations
• That same line must be 5 feet from potable water lines and stormwater lines. It is exempt where every part of the water or stormwater line within 5 feet runs at least 12 inches above the top of the effluent line. That part must also be sealed inside a sleeve of schedule 40 PVC or stronger, or be schedule 40 PVC itself

The unobstructed land a drain field has to have

Rule 62-6.005 asks for suitable, unobstructed land, so the system can be installed and can work properly. The minimum unobstructed area must be at least 1.5 times the drain field absorption area the rule requires. The drain field is counted inside that total, not beside it. Unobstructed soil between drain trenches counts toward it as well.

The rule gives its own example. Where a 200 square foot drain field is required, the total unobstructed area comes to 300 square feet, and the 300 includes the 200. That land must be contiguous to the drain field. It is required in addition to the setbacks in subsections (1), (2) and (3).

Put the two together and it is clear why a lot that looks big enough often is not. The setbacks come out of the usable area first. What is left has to hold the drain field the rule requires, and half as much again in unobstructed land.

There is a relief route when the rules cannot be met. DEP may grant a variance in a hardship case. A variance can be less restrictive than section 381.0065 of the Florida Statutes and the parts of Chapter 62-6 that carry it out. DEP grants one only when three things are true. The hardship was not caused on purpose by the applicant. No reasonable alternative for treating the sewage exists, with cost among the factors weighed. The discharge will not harm the health of the applicant or the public, and it will not significantly degrade groundwater or surface water.

When a conventional system is no longer an option

In 2023 the Legislature passed House Bill 1379, which became Chapter 2023-169, Laws of Florida. It is an environmental protection act, and the septic rule is one provision in it. The Governor approved it on 30 May 2023, and it took effect on 1 July 2023. It changed what may be installed inside three kinds of water quality plan area.

The three are named in the statute. They are a basin management action plan area, a reasonable assurance plan and a pollution reduction plan. Inside them, the sewer decides what is allowed. Where connection to a publicly owned or investor-owned sewerage system is available, a new onsite system is prohibited. Where that connection is not available, the rule is different. A lot of 1 acre or less must then have an enhanced nutrient-reducing system. The state shortens that to ENR-OSTDS. The statute allows another way as well. Any other wastewater treatment system that reaches at least 65 percent nitrogen reduction can be used.

The statute sets a performance standard, not an equipment list. A system qualifies if the department approves it for at least 50 percent total nitrogen reduction before the drain field. It also qualifies at 65 percent or more across the tank or tanks and the drain field together. The statute names no system types. The Department of Environmental Protection names three that can meet the standard.

DEP calls the covered ground the impacted areas. Its fact sheet defines them as all Basin Management Action Plan areas and all Alternative Restoration Plan areas. In that fact sheet DEP names ten Florida counties that contain no area impacted by HB 1379. Nassau is one of the ten. Duval, Clay, Putnam and St. Johns are not among them. DEP says the ten are the only counties without an impacted area, so each of the other four holds some. Which parts is a question about the lot, not the county. That fact sheet is version 1.0b, dated February 2025, and it describes the areas as they stood then. Chapter 62-6 still applies in all ten counties.

DEP publishes a mapping tool for this. It is called BMAPs and Alternative Restoration Plans - OSTDS Requirements. A county can be impacted in part, so the address is what settles it.

The statute applies to new systems. DEP says the usual septic variance process is closed to this requirement. That is the process in section 381.0065(4)(h) of the Florida Statutes. DEP names another route in the same answer. A person impacted by the requirement may petition for an administrative hearing. That route is set by sections 120.569 and 120.57 of the Florida Statutes. The hearing can change the agency’s decision. Nothing is final until the department issues a further order. That answer is DEP’s, in its ENR guidance document, version 1.1a, dated 19 December 2023.

• In-ground nitrogen-reducing biofilters
• Florida-approved nitrogen-reducing aerobic treatment units, NSF 245-certified
• Florida-approved nitrogen-reducing Performance-Based Treatment Systems

Who permits a well, and the exceptions

Across most of Northeast Florida, well construction falls under the St. Johns River Water Management District, and the rules are Chapter 40C-3 of the Florida Administrative Code, titled Water Wells, and Chapter 62-532, titled Water Well Permitting and Construction Requirements. The District does not take the application, though. It delegates well permitting — sixteen agreements with local health departments and one with the City of Jacksonville — and those agreements cover every well in the District that the District does not permit itself. So in Clay, Nassau and St. Johns you apply to the county health department. The District still permits wells six inches or greater in outside diameter at land surface.

Duval County is different. Wells under six inches in diameter are permitted by the City of Jacksonville Environmental Quality Division under Chapter 366 of the city Ordinance Code and EPB Rule 8 — not by the water management district. Wells six inches or greater in outside diameter at land surface still goes to SJRWMD. Union County is different in the other direction. It is not in the St. Johns district at all. It sits in the Suwannee River Water Management District, and that district issues the well permit itself, under Chapter 40B-3 of the Florida Administrative Code. There is no county health department step on the well side there. Baker County is the third case. Section 373.069 of the Florida Statutes describes each district boundary in words, and two of those descriptions trace the same line through Baker County. It follows a range line and a township line rather than the county line, so the county is divided between the two districts. On the St. Johns side the Florida Department of Health in Baker County issues the permit under the delegation. Which side a particular property falls on is a question for the districts.

So a Jacksonville homeowner and a Fernandina Beach homeowner drilling the same well apply to two different agencies. If you have been sent to the wrong one, that is why.

Selling or buying a home on septic

There is no statewide Florida requirement for a septic inspection when a house changes hands, and no state-issued "closing letter" for a septic system. If someone has told you the state requires one, they are describing a lender or contract condition, not a law.

What does bind a seller is disclosure. Known material defects affecting value have to be disclosed, and a failing drain field or a system that has been backing up is exactly that. The practical risk is not the state — it is a deal falling apart late because nobody looked.

In practice the inspection gets asked for anyway, by the buyer, the lender or the insurer, and it is normally the buyer paying. That is the point of getting it done early rather than three days before closing, when a drain field problem has nowhere left to go in the schedule.

Being connected to sewer against your wishes

This one is specific to Duval County and it is the question we get asked most often in Jacksonville. It is covered on the Jacksonville page, along with which neighborhoods are in the program and what it costs a homeowner — which, in the JEA and City of Jacksonville program, is nothing up front.

Elsewhere in the region the question rarely comes up, because no comparable program is running in the other counties we cover.