i have used my well water in my reef in the past (for 1.5 years) with no problems, but since upgrading (merged tanks with the bf) and investing many k's into our livestock we have switched to store bought RO water (the 5gal drinking jugs) to be safe
and so we know exactly what is going on with our water chemistry, and it has paid off.
however we plan to use well water again once we get our new FOWLR up and running, it will just have easy softies (shrooms, anthelia etc) and of course fish.
oh and we use well water in our bio-cube, but it hasnt anything other than shrimp in it so thats why.