Some friends of mine lived in Australia for a few years and used
a rooftop cistern for all their water. The wife of the couple is a
hydrologist and did frequent testing of the water. Only in the first
rain of the season did contamination of any consequence occur. They
were in an arid part of the country.

On the subject of filtration, an inexpensive method is a biosand
filter. The schmutzdecke layer of biological material that forms
on the top will eat up heavy metals, bacteria, virus, etc to a high
degree.

http://en.wikipedia.org/wiki/Slow_sand_filter

I have a friend who started this organization for household
bio-sand filters for people in Haiti.
http://cleanwaterforhaiti.org/Design/HTML/filter.html

He works here
http://www.cawst.org/
and you can go take a training class from them.