Who issues your well permit depends entirely on which county the lot is in

The rule, and who enforces it

Every water well in Florida is constructed, modified and abandoned under Chapter 62-532 of the Florida Administrative Code, and the contractors who do that work are licensed under Chapter 62-531. Both chapters belong to the Department of Environmental Protection, but the permits themselves are issued by the five water management districts, and the districts in turn delegate residential permitting where a local agreement exists.

For the counties around Jacksonville that district is the St. Johns River Water Management District, whose rules sit in Chapter 40C-3. It holds delegation agreements with the health departments of Baker, Clay, Nassau, Putnam, St. Johns and Volusia counties among others, and with one local government: the City of Jacksonville.

Duval is the odd one out

In Duval County a well permit is issued by the City of Jacksonville's Environmental Quality Division, not by a health department and not by the District. It is the only delegation to a city government in the whole district, and it is why a Jacksonville homeowner on a well and a septic tank files the well permit in one building and the septic permit in another.

Everywhere else on this company's map, St. Johns, Clay, Nassau, Putnam, Baker and Volusia, the county health department issues both the well permit and the septic permit, which is simpler even if the two permits sit under different rule chapters.

Two counties in two districts

Putnam and Baker each have a western portion inside the Suwannee River Water Management District rather than the St. Johns River district. A parcel out toward those county lines answers to Chapter 40B-3 rather than 40C-3, and the district boundary does not follow any road. Confirming which district a parcel sits in is a parcel-number question, and it is asked before filing, not after.

Filing with the wrong district is not a delay of a few days. It is a rejected application and a fresh start.

When the District permits directly

Wells of six inches or greater outside diameter at land surface are permitted by the St. Johns River district itself regardless of county. Ordinary residential and irrigation wells fall below that and go through the delegated office. Larger irrigation, agricultural and public supply wells are the ones that go to the District.