For more than seven years, Preet Bharara, the United States attorney for the Southern District of New York, made a name for himself as one the nation’s most aggressive and outspoken prosecutors of public corruption and Wall Street crime.

With Mr. Bharara, 48, being told on Friday to step down from his post, it was unclear what effect his expected departure might have on the office’s current investigations.

In past presidential transitions, the storied office, long known to be so independent of Washington that some people referred to it as the Sovereign District of New York, has in large measure moved forward unaffected by politics. Under Mr. Bharara, the office prosecuted Democratic and Republican officials with equal ardor, most notably Sheldon Silver, the former Democratic speaker of New York’s Assembly, and Dean G. Skelos, the former Republican majority leader of the State Senate.

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His office is preparing to try a group of former aides and associates of Gov. Andrew M. Cuomo in a wide-ranging bribery and bid-rigging case and has been investigating Mayor Bill de Blasio’s campaign fund-raising as part of an inquiry into whether he or other officials exchanged official acts for political donations.

The investigation into Mr. de Blasio’s fund-raising, perhaps the office’s highest profile continuing inquiry, began roughly a year ago and appears to be in its final stages, with prosecutors and F.B.I. agents interviewing the mayor for four hours two weeks ago. The mayor’s press secretary said at the time that Mr. de Blasio was cooperating in the inquiry and that “at all times the mayor and his staff acted appropriately and well within the law.”

Investigators have scrutinized scores of donors to the mayor’s 2013 campaign and his now defunct political nonprofit, seeking to determine whether anyone received favorable city action in exchange for their largess.

And with the mayor gearing up for his re-election campaign — he is now seeking to raise the bulk of his war chest from smaller donors — his lawyers are pressing prosecutors to conclude the investigation or, they say, risk affecting the election’s outcome.

It remains unclear whether Mr. Bharara and his top aides have determined whether they will seek charges — against the mayor, any of his top aides or his primary fund-raiser.

Under Mr. Bharara’s stewardship, the office was also known for its insider trading investigations, civil rights cases and terrorism prosecutions.

Another pending investigation appears to focus on how Fox News structured settlements of claims brought by network employees.

Mr. Bharara would presumably be succeeded temporarily by his deputy, Joon H. Kim, a longtime prosecutor and former head of the office’s criminal division.

Also on Friday, the United States attorney for New Jersey, Paul J. Fishman, said in a statement that his resignation had been requested; and in Brooklyn, Robert L. Capers, said he had been “instructed to resign.”

Mr. Bharara had not issued a statement as of Friday evening, when his office was uncertain whether the resignation request applied to him. The announcement that he had been told to resign along with 45 other United States attorneys around the country comes little more than three months after he met with Donald J. Trump, then president-elect, at Trump Tower, and announced afterward that Mr. Trump had asked him to stay on as the United States attorney.

Speaking to reporters after the meeting, Mr. Bharara said that Mr. Trump had asked to see him to discuss “whether or not I’d be prepared to stay on as the United States attorney to do the work as we have done it, independently, without fear or favor for the last seven years.”

“We had a good meeting,” Mr. Bharara said. “I said I would absolutely consider staying on. I agreed to stay on.”

Mr. Bharara also said at the time that he had already spoken with then-Senator Jeff Sessions, the Republican of Alabama who Mr. Trump appointed attorney general. “He also asked that I stay on, and so I expect that I will be continuing,” Mr. Bharara said.

Among the names of lawyers mentioned as a possible United States attorney in Manhattan in the Trump administration is Marc L. Mukasey, a former Southern District prosecutor and the son of Michael B. Mukasey, the former attorney general in the Bush administration. The younger Mr. Mukasey is now a lawyer at Greenberg Traurig, a law firm in New York where Rudolph W. Giuliani, a close associate of Mr. Trump, also works. Mr. Mukasey declined to comment on Friday.

Mr. Bharara is no stranger to politics: before being appointed United States attorney by President Barack Obama in 2009, he served as chief counsel to Senator Charles E. Schumer, Democrat of New York, and played a major role in the Senate Judiciary Committee’s investigation into the politically motivated firings of United States attorneys by the Justice Department under President George W. Bush.

If there is a “credible whiff that justice has been politicized,” Mr. Bharara told The New York Times in 2014, “there’s nothing worse than that.”

Ben Protess and Matthew Goldstein contributed reporting.

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