Alachua County handles building permits for unincorporated areas and several smaller municipalities that contract for services. The City of Gainesville operates its own independent building department and permitting portal for properties within city limits. Development in the county is subject to specific environmental protections, including the Alachua County Comprehensive Plan and various wetland and aquifer protection overlays.
How this fits with the state
The state authority here is Florida DBPR - Construction Industry Licensing Board. The county file does not replace that — it adds the permit office, local overlays, and the actual filing path.