Personally as long as you discard the "first flush" when it rains and filter the rain water will be OK. (google for rain water first flush to see what is required).
There are many ponds, lakes, water ways, nature reserves, water reservoirs (eg Heathrow) all under flight paths and they clearly don't have any issue with water contamination. I regularly walk under the nature reserve under Eastleigh airport approach path and ponds & rivers are teaming with life.