The county handles permitting for all unincorporated areas, while the cities of St. Augustine and St. Augustine Beach maintain their own independent building departments. Projects in unincorporated areas are subject to specific coastal construction control lines and extensive flood zone regulations due to the county's Atlantic coastline and St. Johns River frontage.
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.