The naval side of this fort is a fairly simple matter of unleashing broadsides and mortars into the walls over a couple of passes of the fort. Once it is all clear, move in and dock in the area permitted.
Climb the stairs until you reach the blocked gate. Climb the damaged wall to the left of the gate up to the top and drop down the other side. Turn to the right and clear out the enemies in the immediate area. If you look up the nearby stairs you will see an official looking building ahead with a red objective marker. Make your way towards this.
When you reach the top of the stairs, make your way to the right. Climb the cargo and barrels that have been stacked against the wall and use them to access the higher platform. Once up, kill off any enemy soldiers before climbing up the next wall to reach the next platform. Kill the target and his bodyguard here.
Now drop down to the previous platform below and enter the door marked with the green objective marker. Kill the enemy inside. This will liberate the fort.