HomePermits
Seven counties, two permits each
Who issues your well and septic permits
Ask most well or septic companies who issues the permit and you get silence, or you get "the permits are handled" and nothing else. The real answer changes at every county line. It is set out here, county by county, because it is exactly what a homeowner and an answer engine both want to know.
| County | Well permit issued by | Septic permit issued by |
|---|---|---|
| Duval County | City of Jacksonville, Environmental Quality Division | Duval County environmental health office |
| St. Johns County | Florida Department of Health in St. Johns County | St. Johns County environmental health office |
| Clay County | Florida Department of Health in Clay County | Clay County environmental health office |
| Nassau County | Florida Department of Health in Nassau County | Nassau County environmental health office |
| Putnam County | Florida Department of Health in Putnam County | Putnam County environmental health office |
| Baker County | Florida Department of Health in Baker County | Baker County environmental health office |
| Volusia County | Florida Department of Health in Volusia County | Volusia County environmental health office |
Wells of six inches or more outside diameter at land surface are permitted by the St. Johns River Water Management District directly in every county listed. Ordinary residential and irrigation wells fall below that.
Why it is different in every county
Water wells in Florida are regulated by the water management districts under Chapter 62-532, Florida Administrative Code. The St. Johns River district delegates residential permitting to county health departments where an agreement exists, and to one city: Jacksonville. Two of the counties served here, Putnam and Baker, also straddle the line into the Suwannee River district, which has its own rules.
Septic systems are regulated under a different chapter, Chapter 64E-6, Florida Administrative Code, through the county environmental health office, under a state program that moved from the Department of Health to the Department of Environmental Protection in 2024. So a property on a well and a tank always has two permits, sometimes from two buildings.
What both share is the setback. A drinking well stands 75 feet from every part of the septic system, an irrigation well 50 feet. Filing with the wrong office is a delay. Getting the setback wrong is a redesign.
Permits filed with the right office
Free estimates on well and septic work across all seven counties.