The province's Disease Control Laboratory will test for bacteria and the Water Security Agency will assess flooded wells and cisterns to see if the water is still potable.
Health Minister Dustin Duncan says preventing waterborne diseases is an effective way to help protect the public.
The free water testing will be available from now until the end of the flood season.
Residents can contact their local health regions to find out if they are eligible for the tests and to obtain forms and sample containers.
The water agency is forecasting above normal or well-above-normal runoff in the entire southern half of Saskatchewan.