As with Ambergris Key, this smuggler location is marked by and entered using a sunken ship. As such, sail over to the San Juan marker on the world map and dock with the shipwreck to dive underwater.
Leave the diving bell and swim forward into the tunnel . As you work your way through it, be careful to stay away from the walls due to an abundance of urchins. Keep moving through the tunnel, and grab the Animus Fragment as you go, and keep swimming until you reach the first air pocket. Surface in here to replenish your air.
Follow the next tunnel until you reach a larger room at the end. Loot the chest in here and then follow the next short set of tunnels until you surface in the smuggler’s cavern.
Swim over and climb the wooden structure on the right. Perform a ledge assassination on the enemy at the top. Next, climb up and knock out the other bad guy in front. Loot the chest here. Climb the wall to the right of his position and climb up onto the ledge.
Walk out across the top of the room using the rope strung up here. When you are around halfway across, look down to the right and perform an air assassination on the guard by himself on the north side of the room. Loot the chest he was guarding. Double assassinate the pair of enemies looking at the wall to the left of the chest.
Climb the ladders all the way to the top and grab the Animus Fragment from the small beam. Take care of the Gunners here. Run through the short cave and dive into the water below. Swim over to the Jackdaw.