When I double w while underwater to swim faster I can reach the shore and swim into the first layer of sand. I then seem to be half as tall and can not jump out of the sand onto the next level. If I dig onto the sand next to me then it drops me down one block if i want to go there.  I then have to dig back to the water and get away from shore before it will return to a normal height of character.

My guess is that swimming makes the character horizontal and it isn't reverting back to vertical once I hit the sand.