Lake Santa Fe
On Lake Santa Fe, the following activities require a permit:

Dredging or filling, on or near the lake:

U.S. Army Corps of Engineers - Jacksonville
permitting: 904-232-1666
dredging: 904-232-2071

Florida Department of Environmental Protection
permitting: 904-807-3300

Suwannee River Water Management District
permitting: 800-226-1066

Alachua County Environmental Protection Dept.
permitting: 352-264-6800

Construction of docks, sea walls, boat ramps or water ward structures
(for property in all counties on the lake):

Florida Department of Environmental Protection
permitting: 904-807-3300

Suwannee River Water Management District
permitting: 800-226-1066

Alachua County Environmental Protection Dept.
permitting: 352-264-6800

Removal or alteration of aquatic or shoreline vegetation (including trees):
 
Florida Fish and Wildlife Conservation Commission, Aquatic Plant Management
Suwannee River Field Office - 3377 East US Highway 90, Lake City, FL 32055    386-758-0525
For all persons interested in controlling or removing aquatic vegetation from the lake, the required FWC Aquatic Plant Removal Permit Application is available HERE.
 
Alachua County Environmental Protection Dept.
permitting: 352-264-6800

Installation or repair of septic systems:

Alachua County Health Dept.:
352-334-7930

Bradford County Health Dept.:
904-964-7732

Clay County Health Dept.:
352-269-6341 x148

Putnam County Health Dept.:
386-326-3200