There are a few methods that can be used to kill microbes that might be present in water. These include heating, UV treatment and the use of chemicals such as chlorine.
In the document below there are links about each of these and a summary sheet to be completed.
Answers can be seen here.
To judge the amount of bacteria present in a water sample the following experiment can be carried out.
Maybe sunlight is the answer? This video will let you find out more about SODIS - using sunlight to purify water.
General videos about microbes in water and how to clean it.