The water "goes over" the land, when the land is actually above the water. The water seems to override everything else in that aspect, as does the sky...
Can anybody help me out? I'm new to the G.E.C.K., but I did a lot in the Elder Scrolls Construction Set for Oblivion and never ran into this problem.
Edit. I fixed it, I needed the Water LOD to be the same as the water height... could've sworn I did that but I guess I forgot to. Getting this closed.