Woodward explained that when he wanted to meet Deep Throat, he would move a flowerpot with a red flag on his apartment balcony; he lived at number 617, Webster House, 1718 P Street, North West. On occasions when Deep Throat wanted a meeting, he would circle the page number on page twenty of Woodward's copy of The New York Times (delivered to his building) and draw clock hands to signal the hour. Adrian Havill questioned these claims in his 1993 biography of Woodward and Bernstein. He said Woodward's balcony faced an interior courtyard and was not visible from the street. Woodward said that the courtyard had been bricked in since he lived there. Havill also said The Times was not delivered in copies marked by apartment, but Woodward and a former neighbor disputed this claim.

Born on August 17, 1913, in Twin Falls, Idaho, Felt was the son of Mark Earl Felt and his wife, the former Rose R. Dygert. His father worked as a carpenter and building contractor. His paternal grandfather was a Free Will Baptist minister. His maternal grandparents were born in Canada and Scotland, respectively. Through his maternal grandfather, Felt was descended from Revolutionary War general Nicholas Herkimer of New York State.

After graduating from Twin Falls High School in 1931, Felt attended the University of Idaho in Moscow, Idaho. He was a member and President of the Gamma Gamma chapter of the Beta Theta Pi fraternity. He received a BA in 1935.

Felt went to Washington, D.C., to work in the office of Democratic U.S. Senator James P. Pope. In 1938, Felt married Audrey Robinson of Gooding, Idaho, whom he had known when they were students at UI. She had come to Washington to work at the Bureau of Internal Revenue. Their wedding was officiated by the chaplain of the United States House of Representatives, the Rev. Sheara Montgomery. Audrey, who died in 1984, and Felt had two children, Joan and Mark.

Felt stayed on with Pope's successor in the Senate, David Worth Clark (D-Idaho). He attended the George Washington University Law School at night, earning his law degree in 1940, and was admitted to the District of Columbia bar in 1941.

He applied for a job with the FBI in November 1941 and was accepted. His first day at the Bureau was January 26, 1942.

The Espionage Section was abolished in May 1945 after V-E Day. After the war, Felt was assigned to field offices, first to Seattle, Washington. After two years of general work, he spent two years as a firearms instructor and was promoted from agent to supervisor. Upon passage of the Atomic Energy Act and the creation of the United States Atomic Energy Commission, the Seattle office became responsible for completing background checks of workers at the Hanford plutonium plant near Richland, Washington. Felt oversaw those investigations. In 1954, Felt returned briefly to Washington as an inspector's aide. Two months later, he was sent to New Orleans, Louisiana, as Assistant Special Agent-in-Charge (SAIC) of the field office. When he was transferred to Los Angeles, California, fifteen months later, he held the same rank there.

In 1956, Felt was transferred to Salt Lake City, Utah and promoted to Special Agent-in-Charge (SAC). The Salt Lake Office included Nevada within its purview. Felt oversaw some of the Bureau's earliest investigations into organized crime, assessing the Mob's operations in the Reno and Las Vegas casinos. (It was Hoover's, and therefore the Bureau's, official position at the time that there was no such thing as the Mob.) In February 1958, Felt was assigned to Kansas City, Missouri (which he dubbed "the Siberia of field offices" in his memoir), where he directed further investigations of organized crime. By this time, Hoover had come to believe in organized crime, in the wake of the famous Apalachin, New York, conclave of underworld bosses in November 1957.

Felt returned to Washington, D.C., in September 1962. As assistant to the bureau's assistant Director in charge of the Training Division, Felt helped oversee the FBI Academy. In November 1964, he was promoted to an Assistant Director of the Bureau, as Chief Inspector of the Bureau and Head of the Inspection Division. This division oversaw compliance with Bureau regulations and conducted internal investigations.

In his memoir, Felt strongly defended Hoover and his tenure as Director; he condemned the criticisms of the Bureau made in the 1970s by the Church Committee and civil libertarians. He also denounced the treatment of Bureau agents as Criminals and said the Freedom of Information Act and Privacy Act of 1974 served only to interfere with government work and helped Criminals. (He opens the book with the sentence, "The Bill of Rights is not a suicide pact", Justice Robert H. Jackson's comment in his dissent to Terminiello v. City of Chicago, 337 U.S. 1 (1949)).

On July 1, 1971, Felt was promoted by Hoover to Deputy Associate Director, assisting Associate Director Clyde Tolson. Hoover's right-hand man for decades, Tolson was in failing health and unable to carry out his duties. Richard Gid Powers wrote that Hoover installed Felt to rein in william C. Sullivan's domestic spying operations, as Sullivan had been engaged in secret unofficial work for the White House. In his memoir, Felt quoted Hoover as having said, "I need someone who can control Sullivan. I think you know he has been getting out of hand." In his book, The Bureau, Ronald Kessler said that Felt "managed to please Hoover by being tactful with him and tough on agents." Curt Gentry described Felt as "the director's latest fair-haired boy", who had "no inherent power" in his new post, the real number three being John P. Mohr.

Haldeman later initially suspected lower-level FBI agents, including Angelo Lano, of speaking to the Post. But in a taped conversation on October 19, 1972, Haldeman told the President that sources had said that Felt was speaking to the press.

In June 1973, Ruckelshaus received a call from someone claiming to be a New York Times reporter, telling him that Felt was the source of this information. On June 21, Ruckelshaus met privately with Felt and accused him of leaking information to The New York Times, a charge that Felt adamantly denied. Ruckelshaus told Felt to "sleep on it" and let him know the next day what he wanted to do. Felt resigned from the Bureau the next day, June 22, 1973, ending his thirty-one year career.

Jack Limpert published evidence as early as 1974 that Felt was the informant. On June 25 of that year, a few weeks after All the President's Men was published, The Wall Street Journal ran an editorial, "If You Drink Scotch, Smoke, Read, Maybe You're Deep Throat." It began "W. Mark Felt says he isn't now, nor has he ever been Deep Throat." The Journal quoted Felt saying the character was a "composite" and "I'm just not that kind of person." In 1975, George V. Higgins wrote: "Mark Felt knows more reporters than most reporters do, and there are some who think he had a Washington Post alias borrowed from a dirty movie." During a grand jury investigation in 1976, Felt was called to testify. The prosecutor, J. Stanley Pottinger, Assistant Attorney General for Civil Rights, discovered that Felt was "Deep Throat", but the secrecy of the proceedings protected the information from being public.

When Felt was called to testify in 1975 by the U.S. House about the destruction of Hoover's papers, he said, "There's no serious problems if we lose some papers. I don't see anything wrong and I still don't." At the same hearing, Gandy claimed that she had destroyed Hoover's personal files only after receiving Gray's approval. In a letter submitted to the committee in rebuttal of Gandy's testimony, Gray vehemently denied ever giving such permission. Both Gandy's testimony and Gray's letter were included in the committee's final report.

The Church Committee of Congress revealed the FBI's illegal activities, and many agents were investigated. In 1976, Felt publicly stated he had ordered break-ins, and recommended against punishment of individual agents who had carried out orders. Felt also stated that Patrick Gray had also authorized the break-ins, but Gray denied this. Felt said on the CBS television program Face the Nation he would probably be a "scapegoat" for the Bureau's work. "I think this is justified and I'd do it again tomorrow," he said on the program. While admitting the break-ins were "extralegal", he justified them as protecting the "greater good." Felt said:

Griffin B. Bell, the Attorney General in the Jimmy Carter administration, directed investigation of these cases. On April 10, 1978, a federal grand jury charged Felt, Miller, and Gray with conspiracy to violate the constitutional rights of American citizens by searching their homes without warrants.

After the revelation, publishers were interested in signing Felt to a book deal. Weeks later, PublicAffairs Books announced that it signed a deal with Felt. Its CEO was a Washington Post reporter and Editor during the Watergate era. The new book was to include material from Felt's 1979 memoir, plus an update. The new volume was scheduled for publication in early 2006. Felt sold the movie rights to his story to Universal Pictures for development by Tom Hanks's production company, Playtone. The book and movie deals were valued at US $1 million. A film based on those rights, Mark Felt: The Man Who Brought Down the White House, in which Felt is portrayed by Liam Neeson, was released in 2017.

The jury returned guilty verdicts on November 6, 1980. Although the charge carried a maximum sentence of 10 years in prison, Felt was fined $5,000 and Miller was fined $3,500. Writing an OpEd piece in The New York Times a week after the conviction, attorney Roy Cohn claimed that Felt and Miller were being used as scapegoats by the Carter administration and it was an unfair prosecution. Cohn wrote the break ins were the "final dirty trick" of the Nixon administration, and there had been no "personal motive" to their actions. The New York Times praised the convictions, saying "the case has established that zeal is no excuse for violating the Constitution."

In a phone call on January 30, 1981, Edwin Meese encouraged President Ronald Reagan to issue a pardon. After further encouragement from Felt's former colleagues, President Reagan pardoned Felt and Miller. The pardon was signed on March 26, but was not announced to the public until April 15, 1981.

Despite their pardons, Felt and Miller won permission from the United States Court of Appeals for the District of Columbia Circuit to appeal their convictions so as to remove it from their record and to prevent it from being used in civil suits by victims of the break-ins they had ordered. Ultimately, the court restored Felt's law license in 1982, based on Reagan's pardon. In June 1982, Felt and Miller testified before the Senate Judiciary Committee's security and terrorism subcommittee. They said that the restrictions placed on the FBI by Attorney General Edward H. Levi were threatening the country's safety.

The identity of Deep Throat was debated for more than three decades, and Felt was frequently mentioned as a possibility. An October 1990 Washingtonian magazine article about "Washington secrets" listed the 15 most prominent Deep Throat candidates, including Felt.

In 1992, James Mann, who had been a reporter at The Washington Post in 1972 and worked with Woodward, wrote a piece for The Atlantic Monthly, saying the source had to have been within the FBI. He noted Felt as a possibility, but said he could not confirm this.

Leonard Garment, President Nixon's former law partner who became White House counsel after John W. Dean's resignation, ruled Felt out as Deep Throat in his 2000 book In Search of Deep Throat. Garment wrote:

In 2002, the San Francisco Chronicle profiled Felt. Noting his denial in The FBI Pyramid, the paper wrote:

In mid-2005, Woodward published an account of his contacts with Felt, The Secret Man: The Story of Watergate's Deep Throat (ISBN 0-7432-8715-0).

Felt died at home, in his sleep, on December 18, 2008. He was 95 years old and his death was attributed to heart failure.

In his 2012 book Leak: Why Mark Felt Became Deep Throat, Max Holland argued that Felt leaked the information in an attempt to become head of the FBI. Holland said that Felt wanted to create the perception that Gray "could not control the FBI". This could result in Nixon's firing Gray, leaving Felt as the obvious choice to run the agency. Holland said this plan (if it was one) backfired as Nixon and his team found out that Felt was the leaker.

In a 2013 interview, Ruckelshaus noted the possibility that the original caller was a hoax. He said that he considered Felt's resignation "an admission of guilt" anyway.

He later said: "I had been gloriously and illegally deceived, and Deep Throat was, in characteristic style, back in business—which given his history of betrayal, was par for the course."