When I had this problem I just "painted" shallow water over the whole map and started over =D as it's related to cliffs it's sort of hard to find out where the issue is and remove it
The only problem is that there is no water in between, so just place some shallow water cliffs things there and then brush the Same Height thingy, so it isn't shown. Then just lower the ground and you've got water.
Like that; http://www.thehelper.net/forums/showthread.php?t=32674
