Baker County · a county almost entirely on wells
Well and septic permits in Baker County
Who issues the well permit, who issues the septic permit, and what each one turns on for a property in Baker County.
Baker County at a glance
- Well permits
- Florida Department of Health in Baker County
- Septic permits
- Baker County environmental health office
- County seat
- Macclenny
Well permits
Baker County's health department holds a delegation agreement with the St. Johns River district. Baker also straddles a district line, with part of the county inside the Suwannee River district, so a parcel in the far west of the county can fall under a different authority than one in Macclenny.
Construction, modification and abandonment all require a permit under Chapter 62-532, Florida Administrative Code.
Septic permits
Septic permitting runs through the county environmental health office, and on large rural lots the practical constraint is usually the well, the property line and the seasonal water table rather than the space available.
New systems, replacements, repairs to the drain field and tank abandonment are permitted under Chapter 64E-6, Florida Administrative Code.
What that means on the ground
Outside Macclenny and Glen St. Mary there is very little utility water in Baker County at all. A pump failure on the roads north of town is a genuine emergency because there is nothing to fall back on, and a septic failure has the same weight because there is no sewer to connect to instead.
Both permits come from the county health department in Macclenny. Lots are large, so the setback between well and drain field is rarely the problem it is closer to Jacksonville; the seasonal water table on flat ground is the constraint that shapes a drain field design here.
The far west of the county sits in the Suwannee River district rather than the St. Johns River district, which changes the district rules a well answers to. Call Flamingo checks the parcel before filing.
The one number both permits share
A private drinking well has to sit at least 75 feet from any part of a septic system, and an irrigation well 50 feet, under the state onsite sewage rule. Whichever office issues which permit in Baker County, that measurement is what decides where a new well or a new drain field can go. How the setback plays out on a lot.
Straight answers
Baker County permit questions
Who issues a well permit in Baker County?
Florida Department of Health in Baker County. Baker County's health department holds a delegation agreement with the St. Johns River district. Baker also straddles a district line, with part of the county inside the Suwannee River district, so a parcel in the far west of the county can fall under a different authority than one in Macclenny.
Who issues a septic permit in Baker County?
Baker County environmental health office. Septic permitting runs through the county environmental health office, and on large rural lots the practical constraint is usually the well, the property line and the seasonal water table rather than the space available.
Does Call Flamingo handle the permits?
Yes. Well construction, modification and abandonment permits, and septic installation, replacement and abandonment permits are filed with the county office as part of the job, and the completion or abandonment report is filed afterwards.

Well or septic work in Baker County
Free estimates and the permit filed with the right office, seven days a week.
