This is just how JJ2 works. If water has been activated, then ambient lighting affects the water color (although only in 8-bit color mode) but not the lighting for the part of the level that is outside of the water. There is no way to disable this behavior, and moreover, no way to deactivate water within a level once it's been activated. Sorry.

ETA: In the name of being overly helpful, I guess you could try to find the memory addresses used for water and edit them using JJM-Script? I don't know if anyone actually uses JJM, though, and water might not be one of the values it can reliably edit (given that its address doesn't appear to be known).