I read in the National Geographic about a new way to kill the bad stuff in water when there are not a lot of options (chlorine, boiling, filtering, etc...). Solar energy can destroy 99.9% of the microorganisms that cause diseases such as dysentery, cholera and chronic diarrhea (E coli).
Solar water disinfection, also known as SODIS.
Take clear plastic PET bottles wash them out, then with clear water that is not pure, fill them up and set them in the sun for at least 6 hours. You want to get the water hot so you may even put them on a hot metal surface. Not a long term, large scale solution, but great for individuals and families.