[Dumb_Peon]

Hello. Thanks in advance to anyone willing to comment here. My problem is that when applying changes with Noggit to the zones of Un'goro and Thousand Needles some of the the water in the saved areas rises really high in altitude, as show here  https://imgur.com/IHQdumF  and here https://imgur.com/lEHdDn7  . I'm guessing it's because the 2 zones are craters and way bellow the usual altitude of other zones but still I have no idea how to fix this since i've never edited water before and i never learned, the changes done were all not water related as well. 

Any points in the right direction would be appreciated.

[Zarkeven]

I would say just use the lock feature (keybind F) and go over that area, making sure it stays under the terrain. You can also just clear the water that isnt visible by going to that ADT and using the crop water button in the water GUI in noggit.

[wungasaurus]

If I guess right these two options won’t do anything because the water in question isn’t wotlk style water (MH2O) but pre wotlk (MCLQ), which noggit doesn’t properly support and thus break. 
 

I don’t know about the state but maybe more recent versions of noggit no longer break stuff or even convert the water, which would solve this. Of course you‘d either have to redo your edits or modify the water as suggested above.