Key points of World Map - Locations - Assassin's Creed IV: Black Flag
City
An independent location
A fort
A pirate island
A plantation
Isle
Mayan ruins
Underwater location
Smugglers' den
This type of locations become available after you buy the dive bell in the 1st mission of the 6th sequence in the main storyline. They are divided into two groups - near and away from the shore. The first ones include Ambergis Key, San Juan and Anotto Bay, and the other la Concepcion Wreckage, Black Trench, Blue Hole, Kabah Ruins, Atoch Wreck, San Ignacio Wreck. The last one is close to the shore but, in no way does this change its status. The underwater locations need to be sailed up to and moored at in the designated area. After a short cutscene, Edward will go underwater.
The main difference between the above types of locations is that the ones close t the coast are only partially flooded. You need to dive to get to them but, sooner or later, Edward goes out of water. Most often into a cave or ruins. In the case of the locations away from the shore, Edward will constantly be underwater.
There are more differences to follow. In the locations close to the shore, you will encounter pirates and smugglers. While diving, you are deprived of your armor and gear so, you will have to fight them hand to hand, using throwing knives or the obtained weapons. Being without you're your armor, you will have less health bars and the limited space makes it more difficult to flee. Additionally, you can return from such locations over land.
In locations away from the shore, you have no weapons, even your fist. Your enemies are sharks, sea urchins, morays and medusas. You cannot attack sharks so, your only tactic against them is hiding among seaweed and quick swimming. The motionless urchins and medusas that move around small areas, need to be avoided, just like the hidden morays.
In both cases, while underwater, you need to replenish your air, either thanks to air bubbles or barrels with air.
The locations away from the shore reveal their maps right after you visit them, they usually have more chests in them (5 to 8) and Animus Fragments (3), and they shelter one legendary design plan. The other kind are smaller but you need to explore them on your own.