I can just go by what I do, we use our rain water to do water changes in the pond. Every time it rains the pond gets a good water change. We are not on city water, so the cost is not the issue, but with the dry summers and dry winter we have had so far, we want to protect our well. In a different neighborhood a few had dry wells last year.
I have been using roof water since we built the pond, so far the fish, frogs, tads, bugs, snails (trapdoor and others) are doing great. I personally think if the roofing material was introducing toxins, it would be on the banned list. Think of what the trillions of roofs would be doing to the ground water.