Noggit SDL 1.2 and older:
Use AllWater. its shipped with tools pack from getting started tutorials. If you didn't read them, I would suggest you to do so.
Noggit SDL 1.3:
You may use Add water function in Assist menu and adjust your water setting by water modding tool. However, you can't control where will and where won't be water chunk by chunk. For that you may want to use already mentioned AllWater.
Noggit SDL 1.4:
viewtopic.php?f=48&t=8876Its described in main post in new features section. The only one thing you might want to use AllWater when using this version of noggit is when you want to have more water types at one ADT. Thats something what even the newest noggit, sadly, still can't do. Btw, make sure you have the newest version of 1.4 .exe from here:
https://drive.google.com/folderview?id= ... aring#list