CENTRAL ISLIP, N.Y. — For months, Representative George Santos seemed to possess a Teflon-like resistance to repercussions, even as questions mounted over his income, campaign finances and rags-to-riches life story.

Mr. Santos, a first-term Republican representing Long Island and Queens, gave numerous speeches on the House floor and appeared to relish his growing notoriety. Just in the last month, he announced his bid for re-election and tried to leverage his vote with House Republican leadership on a contentious bill to raise the debt ceiling.

But on Wednesday, Mr. Santos was confronted with consequences that may prove difficult to skirt. Federal prosecutors charged him with 13 counts of wire fraud, money laundering, stealing public funds and lying on federal disclosure forms, and took him into custody.

Appearing before a judge and scores of assembled reporters in a federal courthouse in Central Islip, Mr. Santos pleaded not guilty on all charges. Sitting upright, with his arms crossed before him, Mr. Santos, 34, was polite and deferential, cutting a familiar figure in his trademark outfit of sweater beneath a navy blazer.

But outside, before a scrum of news media and observers that included some holding one-word “Lies” signs, his tone changed. “The reality is, this is a witch hunt!” he announced from behind Ray Ban sunglasses.

Addressing reporters, he maintained that accusations against him were politically motivated, and that he would ultimately clear his name.

“I’m going to fight my battle, I’m going to deliver,” he said.

The indictment by federal authorities marked a precipitous turn in the fortunes of a congressman who went from a symbol of Republican resurgence to a scandal-plagued political punching bag.

Prosecutors say Mr. Santos was involved in three separate schemes. The bulk of the indictment focuses on accusations of corruption in Mr. Santos’s political campaign. Prosecutors allege that Mr. Santos and an unnamed associate in 2022 solicited at least $50,000 in donations for what they claimed was a super PAC. Mr. Santos then pocketed the money for personal expenses, including luxury designer clothing and credit card payments, prosecutors said.

The indictment also accuses Mr. Santos of fraudulently applying for and receiving more than $24,000 in pandemic unemployment benefits while he was actually employed, and of knowingly making false statements on financial disclosure forms in order to mislead the public and the House of Representatives.

The charges are unlikely to affect Mr. Santos’s immediate standing in Congress, which is already diminished. Though the indictment led a few more rank-and-file Republicans to join calls for Mr. Santos’s resignation, he said he had no intention of stepping down and would continue to run for re-election.

House Republican leaders, who are overseeing an exceedingly tight Republican majority and face a looming fight over the debt ceiling, largely defended Mr. Santos’s position on Wednesday, although the House speaker, Kevin McCarthy, said that he would not support Mr. Santos’s re-election effort.

“Santos has a lot going on,” Mr. McCarthy said. “I think he has other things to focus on in his life than running for re-election.”

Nonetheless, no action seemed imminent unless Mr. Santos was found guilty.

“He was already removed from all his committees,” Representative Steve Scalise, Republican of Louisiana and the House majority leader, said. “In America, there is a presumption of innocence, but they’re serious charges. He’s going to have to go through the legal process.”

Mr. Santos was released on $500,000 bond that was secured by three people, whose identities were not made public. His travel will be restricted to New York, Washington and places in between, with advance permission required for other trips. His next court appearance is expected on June 30.

Mr. Santos has been besieged by questions about his background, his personal wealth and his campaign finances since last December, when The New York Times and other outlets began reporting on numerous lies about his biography, education and work history that he had told voters on the campaign trail.

Subsequent reporting uncovered questions about how Mr. Santos had handled the finances of an animal rescue charity he had claimed to operate before running for Congress, and how he had mingled his personal business and political campaign. It also found numerous irregularities in the way his campaign spent and raised its funds.

Federal prosecutors charged Mr. Santos with seven counts of wire fraud, three counts of money laundering, one count of theft of public funds and two counts of making materially false statements to the House of Representatives.

Many of the details in the indictment around the $50,000 in misdirected political contributions appeared to closely match reporting by The Times in January. The Times reported that Mr. Santos registered a company, RedStone Strategies, in November 2021 and told donors it was an “independent expenditure” group, or super PAC, as the entity is also described in the indictment.

The indictment refers to two contributors who each gave $25,000 to a company controlled by Mr. Santos after they were told their money would go to his campaign. The indictment did not identify the contributors, but people with knowledge of the matter identified them as Raymond Tantillo, a Long Island businessman who owns a network of car dealerships, and Andrew Intrater, a wealthy investor.

He added that Mr. Intrater was “gratified” that Mr. Santos would have to answer for his lies in court.

The accusations that Mr. Santos fraudulently received unemployment benefits date back to June 2020, as Mr. Santos was making his first run for Congress. Prosecutors said that he applied then for benefits from New York, repeatedly telling the state through April 2021 that he had been unemployed since March 2020. In reality, he was earning $120,000 a year through his employment at a Florida-based investment company, prosecutors say.

Mr. Santos is one of 35 co-sponsors on a House bill that would help states recover fraudulent pandemic unemployment payments.

Mr. Santos also failed to disclose that income on federal financial disclosure forms in both of his congressional campaigns, in 2020 and 2022. In the indictment, prosecutors also accused him of falsely inflating his salary during those campaigns, failing to disclose other income and lying about the amounts in his checking and savings accounts.

If Mr. Santos is convicted of the charges, he could face up to 20 years in prison for the top counts, according to the U.S. attorney’s office, which worked with the F.B.I., the Internal Revenue Service and the Nassau County district attorney’s office to investigate.

But for months, Mr. Santos has denied any criminal wrongdoing, even as he has admitted to lying about going to Baruch College and playing volleyball there and working for prestigious Wall Street firms.

Mr. Santos is also facing investigation by the House Ethics Committee, which is looking at whether he failed to properly fill out required financial disclosure forms, violated federal conflict of interest laws or engaged in other unlawful activity during his campaign.

He also faces a criminal case in Brazil for check fraud that stemmed from an episode in 2008. Court records show that Mr. Santos spent nearly $700 using a stolen checkbook and a false name at a store near Rio de Janeiro. Mr. Santos confessed to the theft in 2010, but the case was paused when police and prosecutors were unable to locate him after he moved to the United States.

A hearing on that case is scheduled to take place on Thursday.

As of Wednesday, there was little indication that Mr. Santos’s recent legal troubles would put a cramp in his re-election bid. Indeed, shortly after securing the bond that will allow him to campaign outside of the state with advance permission, he turned the ordeal into a fund-raising opportunity.

“The fight is real,” he wrote in a Twitter post about of the charges, which included allegations he had defrauded supporters in the past. “I need your support to keep me fighting for freedom.”

Reporting was contributed by William K. Rashbaum and Rebecca Davis O’Brien from New York; Annie Karni from Washington; and Michael D. Regan and Nate Schweber from Central Islip, N.Y.