Days of heavy rains and flooding have swept tons of silt into the Nile River.
The murky brown water has forced the closure of several main water treatment stations.
Egypt is almost entirely dependent on the Nile for drinking water.
Heavy flooding killed 26 people and injured more than 70 across the country, according to health authorities — mostly in four coastal and southern provinces.
In addition to polluting the Nile, the floods caused power outages, displaced hundreds of people, and swept away dozens of cars, particularly in the Red Sea city of Ras Ghareb.
Earlier this week, angry citizens in Ras Ghareb turned away Prime Minister Sharif Ismail who tried to inspect the damage. Residents there blocked his convoy to protest what they saw as poor infrastructure and insufficient government response to the disaster.