The issue of water quality really falls into two major concerns, blue-green algae blooms and Weil's disease. In the case of blue-green algae, if it is known to be present in a stretch of water then avoid it until it is declared clear. This is necessary normally only for a short time whilst the algae blooms, but follow the advice of the local authorities.
For more information on Weils Disease (Leptospirosis) click here
For more information about Salmon under threat (Gyrodactylus Salaris) click here