I ran into the same issues OP. Built palisade walls as far out as possible into deep water, and the enemies swim around them.

Island bases work perfectly; don't even need a wall.

Or you could just 'trick' the enemies. Build a wall around your whole base on land, but leave an area open. Enemies will go to that area, where you might have a field of stakes, trenches they get stuck in, wolf defenders, etc. Sort of like a tower defense entrance maze.