Do sharks attack you if you're using a water vehicle?
From the Far Cry Wiki article on sharks:
Bull Sharks are animals found in oceans of Far Cry 3. They attack when the player is submerged or in the water, but will not attack players mounted on jet skis. When in a certain radius from a shark, and in the water, they become noticeably agitated and make a beeline for their prey.
You can kill sharks by running them over with a boat or jetski or by shooting them from a boat or from land.
Note that a lot of the artifacts in the game are in shark waters, and I think there's also a storyline mission which requires you to dive in shark water.