It seems that the program didnt convert the morrowind water levels. Some caves and dungens are flooded with water.
IIRC, a lot of Morrowind
IIRC, a lot of Morrowind caves had underwater places, or were completely underwater. Are you seeing this in caves around water areas or in places like the middle of the Ashlands?
possible fix
In one of the mods for morroblivion i downloaded (not sure what one) It said if you load morrowind_ob BEFORE oblivion.esm that it fixes hte water issue. Havent tried yet, but just thought i'd put it out there.
I tried that, didn't work =T
I tried that, didn't work =T

Get a spell with water