I love my well water for drinking, but it's very hard (minerals) and makes it difficult to clean the toilet bowl. Or rather, it makes for stains that resist cleaning something fierce. CLR and such don't work, though people assure me they will. Nope. There has got to be something better.
I live in a hard water area too and use a toilet cleaner called Harpic Power Plus. I use it under the rim and at the bottom of the bowl, give it a good scrub and leave it for ten minutes, to let it work. Alternatively, some people have had success using vinegar and lemon juice. The acid cuts through the deposits but you need to be sure you rinse thoroughly after use.