At all locations, you must follow state fishing regulations and on the Merritt Island National Wildlife Refuge (Banana River No Motor Zone and Mosquito Lagoon) you must carry the "free" refuge fishing permit.
The permit can be printed from the Refuge web site or picked up on the north end of the refuge (Baris Cove/Haulover Canal area) and is a simple acknowledgement that you understand the Refuge rules and while the permit is free, the fine is substantial for not possessing a signed permit.
You can also get a copy of the free permit from my other page: Merritt Island Wildlife Refuge fishing permit
All the areas might be closed at times for rocket launches (my rocket launch schedule page is not always up to date) and the Trident Submarine Basin may be closed if a submarine or ship is docked at the pier.
All fishing locations have specific rules as to how many guests may be brought to fish. Guests must be signed in at one of the security checkpoints and obtain a daily fishing pass. . For maps and full list of rules: http://centerops.ksc.nasa.gov/resource/fish.htm