To kayak the entirety of Florida’s coast, you will need permits for Everglades National Park ($10) and the Big Bend (free). They are necessary because these are two very ecologically sensitive places. By requiring permits, the government can regulate of the number of people impacting the wilderness, record the number of people using the wilderness, report those numbers to respective agencies for budgeting and planning, and watch our every move—those fascists! The number of available camping places is also small but having a permit means you're guaranteed a site.
At the town of Carrabelle, the CT turns inland for a brief trek down the Crooked River. It costs $8 to use one of the campsites on this river. This presents a logistical challenge for the thru-paddler, because the fee must be paid in person or by check through the mail (really, a check!), and you must keep your receipt with you when you camp.
Of course, paying in advance through the mail presents the same problem as with the Big Bend—knowing when you will reach the Crooked River is impossible. Visiting the State Forest office in person when you reach Carabelle is problematic because it is very far from town. The official state guide says, "...you can land at the Timber Island public ramp near Carrabelle and walk a little more than a mile to the headquarters." This is wild understatement. The office is much farther—too far to reasonably expect someone to walk.
If you don't want to stealth camp, I recommend taking a zero day in Carabelle and bumming a ride from someone at the Marina or hotel.
A camping permit for the Big Bend is a much more frustrating experience. The Fish and Wildlife Commission requires you to apply for the permit online and in advance. You are expected to indicate
the specific days on which you will arrive at each campsite. But for the CT thru-paddler, there is no way to know exactly when you will reach the Big Bend. In all likelihood, you will be in
violation of your permit when you set up camp at Rock Island, the first campsite in the Big Bend. I was. It can't be helped. Follow this link to get the permit.
For the sake of appearances, get a permit for the Big Bend, but in the weeks leading up to Rock Island, do not adhere rigidly to a schedule in order to keep the dates listed on the permit.
A permit to camp in Everglades National Park can be picked up at the park office in Everglades City. If needed, the permit can be amended at the park office in Flamingo once you reach it. Why would this be the case? I recommend breaking up your crossing of Florida over two days. Islands open for camping within the bay are managed by ENP.