I need a little clarification. You say well water, but then you say it comes from rain water, which would make it cistern water.
These are two different sources that are going to yield chemically very different types of water.
Well water is groundwater, coming from a aquifer under your land. Biologically it should be very pure, low chance of infecting your fish with bacteria or parasites. Depending on where you live, however, well water can be very hard, very alkaline, contain high metal concentrations such as iron, copper that might be tough on fish and plants. Also, it could be contaminated depending on what kind of industry you have near you (and by near I mean miles and miles upgradient that a plume can travel from). An old gas station with a leaking UST might mean BTEX. An old drycleaner might mean TCE. A pig farm might mean high nitrates. If you are getting your well water tested for drinking regularly, it should be okay on these parameters, but doesn't mean it is not high in iron or other metals that could affect fish.
Rainwater, as long as collected in a clean cistern, is going to be chemically clean -actually, chemically too clean. It is going to be slightly acidic, practically no minerals to speak of. You would have to augment it with minerals and adjust the pH.
Of course a lot of this depends on the fish you are keeping. Keep african annual killies like aphyosemion species, and the rainwater may be just their speed. Keep Rift Lake cichlids and the hard well water could be paradise.