That makes sense. I have tried to change the default water height, but it always goes back to zero, which is probably where this fuzzy water layer is sitting by the looks of it. So how do I change the default water height? I'm using MarkarthWaterFlow if that matters at all.
yeah well in most exterior cells it's about -14000 (check in neighbouring cells and/or without mod loaded), so that'd explain that

i've had bugs like that in geck, but none yet in ck (knock on wood), so can't tell you for sure what to do here (except hitting alt-w to toggle water all in all), what helped in geck though was to neverever change placeable water height in render window, but always and only in the water objects 3d-data-tab, numerically. if it got screwed up already, you could only set it to really high up (it only bug-moves upward, never downward) while you worked and reset it to original height when finished.
and you should of course also check the various water settings in ck's preferences