Mr Felt's daughter Joan told the Washington Post that her father "slipped away" in his sleep.
According to the newspaper, he had suffered two strokes in recent years, and his memory of the Watergate era had almost completely vanished because of Alzheimer's disease.
Mystery surrounded the identity of Deep Throat - named after a popular pornographic movie of the time - for decades, until Mark Felt admitted being the source in 2005.
"I'm the guy they used to call Deep Throat," he told the US magazine Vanity Fair in an article that revealed his secret.
Until then, the Washington Post had refused to confirm his identity.
Reporters Bob Woodward and Carl Bernstein had said they would only break their silence after his death.
He secretly guided the journalists as they investigated a burglary at the Democratic National Committee HQ in Washington's Watergate complex in June 1972.
Mark Felt's role as Deep Throat in the Watergate scandal
The break-in was traced to members of a Nixon-support group, the Committee to Re-elect the President.
Further inquiries unearthed a web of political spying, sabotage and bribery that led all the way to the White House and, eventually, President Nixon's resignation.
It is not known exactly why Mr Felt decided to leak damaging secrets but the Washington Post said he detested the Nixon administration's attempts to subvert the FBI's investigations into the crimes and cover ups.
According to the Post, Mr Felt had insisted on remaining completely anonymous, or on "deep background". He was dubbed Deep Throat by a newspaper editor.
Mr Felt is said to have struggled for many years with the consequences of his actions, fearing he betrayed his FBI badge by disclosing government secrets.
Critics called him a traitor for betraying the Commander-in-Chief. His supporters insist Felt was a hero for blowing the whistle on a corrupt administration.
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