I use rainwater runoff from my roof to fill two small ponds in my front
yard. The goldfish, tadpoles, frogs, dogs, plants,etc. all seem to be fine.
I do have a relatively older shingle roof though, I would be concerned if it were newer and possibly toxic tar/oil byproducts might leach out.
(I don't drink the water myself in any case)
As for neutral natural materials like clay/cedar- don't picture any problem with that. Metal painted roofs
should be pretty safe.
If there is any concern that there may be anything leaching out, running the water through some natural filtering materials (sand/charcoal) and/or
through open streams/pools could help with that.