In a separate report, the British-based charity, Tearfund, said that two out of three people in the world would face water shortages by the year 2025.
In a report to coincide with World Water Day, the WHO says that more than a billion people are affected by shortages and contamination, and that more than three million die each year of water-related diseases.
But the WHO says the situation could be greatly improved by using chlorine or even sunlight to kill the tiny organisms that cause disease.
In a separate report, the British-based charity, Tearfund, said that two out of three people in the world would face water shortages by the year 2025.
The charity warned that millions of people would be forced to leave their homes in search of clean water, becoming what it describes as "water refugees".
While water shortages are subjects of debates in the world's driest regions, the WHO says that many countries have plenty of water available.
Chlorine and sunlight
The problem is that it is often not safe to drink - 90% of water-related deaths are caused by contamination, not shortages.
Simple measures such as using chlorine or sunlight to kill the tiny organisms that cause disease could be implemented cheaply.
Chlorination disinfects water, killing bacteria, viruses and protozoa that transmit disease.
Ultraviolet radiation from sunlight also kills bacteria. Richard Helmer, director of the WHO Health and Environment Unit told the BBC that water left in a bottle in very strong sunlight for one to two days, preferably with a black surface behind it, would be disinfected.
"This is a highly reliable method that has been proven to work," he said.
Water-related diseases were virtually unknown in countries like the Maldives which already had chlorination programmes combined with rainwater collection, Dr Helmer added.
Shrinking lakes
Tearfund claimed that the scale of water shortage was already alarming and was getting worse.
Although efficient water management would enable rich parts of the world to cope, poorer countries would suffer massively, it said.
By 2025, Tearfund says, the volume of water needed to produce food is expected to have increased by at least 50%, because of population growth and the demand for higher living standards.
Tearfund claims the growth of water shortages threatens to reduce the global food supply by more than 10%.
Agriculture already takes more than 70% of the world's fresh water, with the proportion rising to more than 90% in Asia and Africa.