Well, if you don't mind loading custom WADs periodically throughout the stage, which isn't something I condone, you can have several COLORMAP lumps in several different WADs and load up the COLORMAP needed for each particular level... they'd mostly be the same basic colors, but with a few tints here and there.
Of course, when you get around to the linedef colormaps, then they resort to the normal colormap, so don't do anything too drastic or it'll all be for naught once you add water.