Imrinfected

Then this is almost certainly a mod issue. There is some mod present which is changing the water heights in these cells. Using "tlc" from console so you can move below the terrain should confirm that there is water in that cell, it's just moved below where it should be. Or, you've somehow turned off water entrely. I will check. Would this problem have any affect on stability?

I have been messing around in the .ini, yes. I don't remember if I changed that, but I don't believe I did. In the places where there are chunks missing from the water, there is nothing there. Unable to swim in it. I'm able to fall down to the bottom by going into this part of the water.

No, the water disappears when I get closer. I didn't make that very clear, sorry. It appears fine from a distance, but when I get closer there are missing spots.

This is quite possibly the largest problem plaguing me. When sailing around aboard my ship, I've noticed that complete chunks of the water aren't there as I get closer to them and the water actually loads. It looks horrible, and I suspect it has something to do with my random crashes. I've disabled most of the mods in my load order to find the problem is still there. Some times it will move to a different area of the water, but ultimately the problem remains. Do any of you have any information or help to offer me pertaining to this topic?