The around 1,350 pupils at the country's most exclusive boarding school, located by the River Thames near Charles' Windsor Castle, had been due to return on Tuesday but recent heavy rainfall meant the sewers would not be able to cope.
"Following extensive flooding in the region, the Thames Water sewers which serve the town of Eton flooded," the school, whose alumni also include two recent former prime ministers - Boris Johnson and David Cameron, said in a statement.
"We are in regular contact with Thames Water as they seek to resolve the situation and we look forward to welcoming boys back as soon as possible."
There has been widespread flooding across Britain caused by recent storms and Thames Water said its local sewer system had been overloaded.
"We are sorry to staff and students who have been impacted," said a spokesperson for Thames Water. "Our teams will be carrying out a clean-up in the coming days once the river levels recede."
The school, founded in 1440 and where fees are about 50,000 pounds ($63,635) a year, said it had moved to remote learning for pupils in the meantime.
($1 = 0.7857 pounds)
(Reporting by Michael Holden, Editing by Kylie MacLellan)
