When used on a regular basis, rainwater can leach or wash out impurities that gather in your soil which comes from your tap water.
But, what happens when rainwater sits around for a period of time and gets stagnant or even worse, it becomes a breeding ground for mosquitoes? What do you do - panic? Of course not.
You either need to dump the water out or add a small amount of bleach to the rainwater. The bleach will kill off any critters but is will also add chlorine which, in turn, can damage plants in large quantities.
So, it's a true to life catch 22. The best way to approach this is by using the rainwater before it turns into a black lagoon.