Impossible Hard Water Stains?

I have rust/hard water stains in my toilet (well water) that will not go away with anything (tried CLR, and all that) except denture tablets. The problem is that the stain has to sit in the water for 15 minutes and the stains go up well above the water level in the toilet. Swishing the water up onto the stains doesn't help since it has to actually sit in the water, so the only thing I can think of is to purposely stop up the toilet, but I'm not sure how to do that on purpose (please don't suggest a really disgusting way of doing this, as I will have to plunge the toilet later!). Does anyone know how I can fill the toilet with WATER ONLY so that I can get the denture stuff to sit on the stain long enough AND I will be able to unclog the toilet later without causing damage? Is there another way to do this without having to stop up the toilet?