REDWOOD CITY, Calif. — A Stanford sailor arrived at the university’s gleaming boathouse to clean out her locker at the end of the school year. The doors would not open.

“Did they change the locks again?” she said with an air of exasperation.

It was a reasonable question. In March, when sailing coach John Vandemoer was fired after being snared in a nationwide admissions scandal, the locks were changed at the Arrillaga Family Rowing and Sailing Center. In April, they were changed again, after men’s rowing coach Craig Amerkhanian was mysteriously fired — late in the season, weeks before his planned retirement.

Stanford’s boating troubles stem from the work of William Singer, the private college consultant who collected millions of dollars in payments from wealthy parents and paid college coaches and athletic administrators to designate nonathletes as recruits for admissions purposes at elite universities. In some cases, the college coaches pocketed the money. In others, Singer, who goes by Rick, made donations to the athletic programs.

Stanford is investigating the scope of the wrongdoing. It has hired the law firm Simpson Thacher & Bartlett to review how its athletes are recruited and how athletics-related gifts are accepted.

The university has reviewed email accounts, phone records and computers of coaches and athletic department staff. It has acknowledged that Singer contacted other coaches at Stanford — Amerkhanian among them. At least one parent indicted in the scandal, a Canadian businessman, also contacted Amerkhanian to discuss a recruiting spot for his son. Stanford maintains it has not unearthed any other cases of admissions fraud, however.

“Stanford is strengthening its internal controls and processes in an effort to prevent something like this from happening again,” E.J. Miranda, a university spokesman, said in a statement.

That Stanford is in this position is startling. It has a $26.5 billion endowment and prides itself on achieving athletic excellence without sacrificing integrity. But the turmoil in these two modestly financed athletic programs, along with another pair of dismissals, has resulted in what has long been seen as the ultimate sin at Stanford — sullying the university’s reputation.

“You didn’t do anything that could tarnish Stanford’s name,” Jay Kehoe, a former head sailing coach, said. “That was definitely the culture.”

When Vandemoer, wearing a navy suit and holding his wife’s hand, walked into a Boston courthouse for a sentencing hearing last month, the lawyers on both sides sparred over the extent of the damage done to Stanford’s reputation.

Since the scheme was revealed in March, federal prosecutors have brought criminal charges against more than 50 people, including coaches, Hollywood actresses and prominent figures from the worlds of law and finance.

Vandemoer, who pleaded to conspiracy to commit racketeering, was the first to be sentenced: six months of home confinement for receiving more than $600,000 from Singer in exchange for designating applicants as sailing recruits. The best-known case involved a student from China whose parents paid Singer $6.5 million.

Vandemoer, who put the money from Singer into a fund that supports Stanford’s sailing program, lost his job and his Stanford housing. He now lives at the vacation home of a Stanford benefactor and coaches privately at a club run by his wife, just a few hundred yards from the Stanford boathouse.

“Stanford is a place that I love,” Vandemoer told reporters last month in front of the courthouse. “I have brought a cloud over Stanford, and for that I’m deeply ashamed.”

The sentencing capped a turbulent few months at Stanford. In March, a week before the admissions scandal broke, James Shirvell, an admissions officer, was fired after police charged him with the attempted murder of his girlfriend while under the influence of LSD. Stanford’s president, Marc Tessier-Lavigne, and provost, Persis Drell, vowed to review the applications Shirvell judged “to assure his assessments were sound.”

Then, in April, Stanford abruptly fired two longtime coaches: Shannon Turley, who oversaw strength and conditioning for all varsity sports, and Amerkhanian, who had planned to retire in August, after his 19th season.

In an interview, Turley, who had been praised for reducing injuries, especially among football players, declined to comment on his firing. But he said that “for any errors of judgment that I may have made at Stanford, I can sleep well at night knowing that I did everything in the best interest of the student-athletes.”

Stanford takes great pride in its athletics program, which for the 25th consecutive year won the NCAA’s Directors’ Cup, the award for overall excellence. The university is also notoriously tight-lipped about personnel matters. Few people were aware of why any of the coaches were dismissed.

“Stanford athletics is a really cold, calculating, bureaucratic organization,” said Olympian Silas Stafford, a rower who graduated in 2008. Noting how Amerkhanian’s firing was publicly described as a retirement, Stafford said: “I would call it cowardice. If there’s really dirt, let it see the sunlight. If there’s not, let him go out in style.”

When Stanford was informed last week that multiple people had told The New York Times that Amerkhanian had been dismissed, it acknowledged he was given a choice — retire or be fired — for violating employee behavior policies. Stanford said the violations came to light this year but refused to specify if they were spurred by the federal investigation or if they were gleaned from the scrubbing of computers and phones.

Amerkhanian, 62, declined to comment.

If sailing requires mental and physical dexterity, reading the wind and the opponent, and moving decisively on a small boat, then Vandemoer, 41, was a fitting avatar: short, serious, hardworking and quiet, with dark sunglasses and a Red Sox cap typically pulled tight over his brow out on the water.

Conversely, rowing requires long levers, brute strength and fierce determination to push through searing pain on the water. If experience is crucial in a sailboat, rowers can be made — and over the last 15 years, few have cranked out Olympians like Amerkhanian.

But some former rowers and Stanford coaches said Amerkhanian could also be territorial, abrasive and a bully.

Stanford suspended him for three months and stripped him of his title as director of rowing during the 2010-11 school year, after a joint Pac-10 and Stanford investigation found violations of school policies and conference rules and abuse of authority, according to what then-athletic director Bob Bowlsby told rowers at the time. Bowlsby, now the commissioner of the Big 12 Conference, declined to comment other than to say the discipline was not connected to admissions.

“He was always a square peg in a round hole in the bureaucracy of Stanford,” said Stafford, who credited Amerkhanian with molding him into an Olympian.

A problem Amerkhanian and Vandemoer had in common was the cost of competing against colleges in the Northeast. In the 2018-19 school year, the sailing team made 15 trips east of the Mississippi River.

According to Department of Education data on operating expenses, Stanford spent $182,000 on its sailing program in 2017 — more than any school other than Boston College and nearly double what Yale and Georgetown spent. But Vandemoer said in an interview before his sentencing that his budget did not include equipment; his biggest fundraising need was to replace a fleet of 18 sailboats — at a cost of about $120,000 — every five to eight years.

The rowing teams do not travel as frequently — or as far — but they have a substantial expense that the sailors do not. They must transport their boats, which can run up to $80,000 for a carbon fiber shell, to races.

Stanford spent about $386,000 on its rowing programs in 2017 — down from a peak of $557,000. Other top rowing programs like Yale and Cal each spent about $675,000 in 2017, and the University of Washington spent $1.25 million.

Though Stanford said its coaches do not have fundraising benchmarks, the external pressures to finance these programs were touched on in letters supporting Vandemoer to the judge who sentenced him. A parent of two Stanford sailors noted that the team stayed at his house in Annapolis, Maryland, to save money.

In addition, Joseph W. McCoy, a Stanford alumnus and avid sailor, wrote: “I am not at all surprised with how such low-profile and poorly funded sports like sailing, soccer, rowing, etc., became such easy targets in this rather ingenious criminal operation that created this mess.”