Last month, federal prosecutors indicted 18 current and former sheriff's deputies for alleged crimes that included beating inmates and jail visitors, falsifying reports, and trying to obstruct an FBI probe of the nation's largest jail system.
U.S. Attorney Andre Birotte Jr. said the indictments showed that "some members of the Sheriff's Department considered themselves to be above the law" and "demonstrated behavior that had become institutionalized."
Baca sidestepped questions about whether he was worried that he might be indicted as part of a federal obstruction of justice probe. "I'm not afraid of reality. I'm only afraid of people who don't tell the truth," he said.
The announcement came as a surprise just weeks after Baca defiantly said the indictments wouldn't drive him from office.
"I don't think anyone expected this," Los Angeles County Supervisor Don Knabe said. "We're all caught a bit off guard."
Because Baca is not serving out his term the five-member Board of Supervisors will be tasked with choosing an interim sheriff. Baca recommended Assistant Sheriff Terri McDonald.
Assistant Sheriff Todd Rogers said after the news conference that he plans to run for office and said Baca's departure was premature but the department's leadership needs a change. Several others had said they would challenge Baca including two former underlings.
"There are reformers in this department and I believe I am one of them," Rogers said.
Baca has acknowledged mistakes while strongly defending his department and distancing himself personally from allegations of misconduct.
The sheriff said he made improvements including creating a database to track inmate complaints. He has also hired a new head of custody and rearranged his command staff.
On Monday, Baca said he would accept the outcome of the FBI investigation but strongly denied criticisms that abuse was rampant.
The American Civil Liberties Union sued the Sheriff's Department in 2012 saying the sheriff and his top commanders had condoned violence against inmates. The organization released a report documenting more than 70 cases of misconduct by deputies.
A federal jury in October found Baca personally liable for $100,000 for failing to stop inmate abuse by deputies in Men's Central Jail in a case brought by a man who said he was severely beaten while awaiting trial.
Last year a Justice Department investigation found deputies made unconstitutional stops, searches, seizures and used excessive force against blacks and Latinos in the Antelope Valley in the outskirts of the county. Baca disputed the findings but said he had instituted reforms.
Baca was criticized in 2007 when he ordered Paris Hilton released from jail under house arrest after serving only few days of a multi-week sentence for driving-related offenses. The sheriff said the socialite developed psychological problems, but a judge put her back behind bars for another 2 1/2 weeks.
A year earlier, Baca had to defend his department's handling of Mel Gibson's drunken driving arrest in Malibu, rejecting claims that deputies tried to cover up anti-Semitic comments made by the actor, who had helped a charity organization for the Sheriff's Department.
The Sheriff's Department also faced recent scrutiny over hiring. The department announced it was reforming hiring practices last month after it was disclosed that 80 deputies had criminal convictions, histories of misconduct or other problem backgrounds. It also gave preferential hiring treatment to friends and relatives of its employees under a special "Friends of the Sheriff" program that allowed top officials to lobby on behalf of applicants, the Los Angeles Times reported.
First elected in 1998 when his incumbent opponent Sherman Block died days before the vote, Baca was re-elected to a fourth term in 2010 and remained a popular figure for much of his time in office.
Less than a year ago he was picked as the nation's sheriff of the year by the National Sheriff's Association, which cited his providing educational opportunities for inmates and efforts to work with religious groups.
The group also noted the vast size of the Sheriff's Department and the relatively low crime rates in areas patrolled by deputies.
The Los Angeles County Sheriff's Department is the largest in the United States, with a staff of 18,000 and a budget of $2.5 billion.
Associated Press Writer Christopher Weber contributed.