Krystal Klear is not a good water substitute. It's designed to make clear flat films, most often in something like an aircraft model where there's a port hole in the fuselage less than 1/4" in diameter, and with skill, tipping some in with a toothpick and doing a sort of soap bubble pop will leave a thin flat film.
As HVH suggests, Envirotex and other epoxy materials, or heat treated materials work. The model railroad people live for this stuff, because their hobby is all about building really really big dioramas. I do that stuff.
But for large scale models where the water area is small, a few ideas. Art stores like Michaels sell Acrylic Matte Medium in various viscosities, in pint jars for about the same cost as 1 ounce of Krystal Klear. This stuff is designed to be painted onto a canvas as a base before painting, to give it a texture. It's like really thick white glue at it's lightest, up to Vaseline in the "Heavy" weight, and can be sculpted before it sets, clear. It's water soluble too for cleanup.
Another possibility is clear silicone sealant, but it really stinks and takes forever to set up.