Is there a place to learn how to do this? MGE doesn't do nice water in interiors (unless that's been improved in the non-stable releases) so this might be a good alternative.
All I did Tchos was lower the non mge, non pixel shader water's transparency to 0,25 (a bit to low tbh) this is in the MW .ini file. And then I vertex colored the sea bottom in different shades of blue all over seydaneen. It looks pretty nice, most of the time. But to much blue yields a bit cartoony look and it's hard to make it look smooth at all times.
The vertex shading can be done in TESCS really easy. It's probably the easiest edit you'll ever try hehe
Also my guess is that does not help interiors at all, almost. :/