Officials say the murky water, now loaded with silt, forced the closure of several main water treatment stations. That has caused the disruption of water supplies in some areas.
Egypt, a mostly desert country of some 92 million, is almost entirely dependent on the Nile for agriculture and drinking water.
Experts warned against drinking tap water for now. Ahmed el-Shennawi, a water expert, told the Rotana Egypt TV network that the "change of the color to yellow is a disaster and we should be cautious until water filtering takes place."
Heavy flooding killed 26 people and injured more than 70 across the country, according 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.
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