When importing, make sure the water edge materials have their transparency set up properly. You can also change the position of the water to where it is based on which lands you have unlocked and show/hide the water edge models depending on the water's height. These are the Y values used by the game:
High (Levels 1-29): 15.3
Mid (Levels 30-40): 13.3
Low (Levels 41-50): 7.46