The captain in a deadly boat accident in New York Harbor this month was arrested by Immigration and Customs Enforcement after an investigation found that he was in the United States unlawfully, the federal authorities said on Wednesday.

The captain, Manuel Hernandez, 46, was initially arrested on Aug. 9, the day after the boat capsized in the harbor, killing a mother and her 5-month-old daughter. A Coast Guard investigation found that the boat was over capacity when it capsized near the Statue of Liberty and did not have life jackets for infants on board, according to a criminal complaint.

Mr. Hernandez was charged on Aug. 10 in Federal District Court in Manhattan with two counts of misconduct and neglect resulting in death. He was released on $50,000 bail. ICE agents arrested him after the Coast Guard’s investigation, the Department of Homeland Security said on Wednesday.

The department said that Mr. Hernandez was from El Salvador and had lied to a Border Patrol officer when he crossed into Texas from Mexico in 2007, falsely claiming to be a U.S. citizen.

“Once he faces justice for his crimes, we will make sure that he is swiftly removed from our country,” Markwayne Mullin, the homeland security secretary, said in a statement.

Mr. Hernandez’s arrest is part of the Trump administration’s broader crackdown on immigration, which administration officials have repeatedly said is necessary to expel criminals from the country.

After a slight dip this spring, ICE arrests have surged in recent weeks as immigration officers face pressure from the White House to meet a goal of 2,000 arrests a day. Although administration officials frequently say they are targeting the “worst of the worst,” their enforcement efforts have swept up many people with no criminal records.

The department did not immediately respond to a request for comment on Thursday.

Mr. Hernandez’s lawyer, Amy Gallicchio, declined on Thursday morning to comment on his arrest or the case. The New York Police Department did not respond to a request for comment.

Mr. Hernandez was piloting a Yamaha AR210 chartered for a birthday celebration on Aug. 8 when it capsized, killing a 27-year-old woman, Sara Sánchez, and her daughter, Antonella.

The boat was carrying 14 people at the time, exceeding its maximum capacity of 10, according to a federal complaint.

Mr. Hernandez said he had borrowed the boat from a friend while his own was out for repairs. A customer paid at least $1,800 for the tour.

As the boat sailed down the East River and into Upper New York Bay, Mr. Hernandez made a U-turn. This ran the boat into a swell, which may have been the wake of a larger ship, according to court documents. When Mr. Hernandez tried to accelerate through the swell, the water broke over the bow, flipping the boat and throwing all 14 passengers overboard.

A dozen passengers climbed onto the overturned hull and were rescued by another boat operated by a tour and Jet Ski rental company. Ms. Sánchez and Antonella were later found by police divers and pronounced dead at nearby hospitals, according to court documents.

Madeleine Ngo contributed reporting.