A couple of articles encourage the use of rainwater to flush toilets. (article 1, article 2)
However, would it be safe to do so if the rainwater in your particular area has a pH that is considered as acidic or akaline?
(The risks of which are outlined on this page and reproduced below)
Best Answer
It is doubtful the pH+ of rainwater anywhere, other than directly downwind of an erupting volcano, would be unsafe in terms of damaging plumbing fixtures or pipes.
That said, there is concern in how the rainwater is stored. It must be kept so as not to be a breeding place for mosquitoes, toxic algae or other noxious critters, nor should the container cause entrapment of wildlife. There also must be air breaks to ensure that the untreated rainwater does not enter and contaminate potable water. There may be local regulations regarding use of rainwater or "greywater".