BOSTON — As Samantha Shelton, an accomplished Harvard swimmer, churned through the water in the 100-yard women’s freestyle on Saturday afternoon, the University of Pennsylvania’s Lia Thomas seemed content to sit on her hip in the adjacent lane.

Shelton chugged ahead from the start, plowing through the water and carrying the lead. But as she did, Thomas cruised along beside her, seeming as unhurried as if on a training swim. Thomas’s broad shoulders and long arms, hallmark features of an elite swimmer, mimicked a windmill with the ease in which they pulled her along.

Then came the final turn.

As Shelton came out of it continuing to fight, on her way to a season-best time, Thomas, with her long, rhythmic, powerful stroke, ate up the margin between them until she had surged past for a near body-length victory. A moment later, the swimmers removed their goggles and acknowledged each other, Thomas reaching over the rope to offer a fist bump to a smiling Shelton.

The gesture might have been nothing more than a nod of appreciation between competitors.

Or it might have been something more symbolic: a signal of acceptance.

So much is open to interpretation each time Thomas jumps into the pool. She is a transgender woman, and has excelled this season while competing on the women’s team. She owns the best marks in the nation among college swimmers in the 200 and 500 freestyle, but for some, her success has also set two pillars of the sporting ethos — inclusion and fair play — in conflict.

Thomas has become a red-meat topic for right-wing media, a divisive matter for L.G.B.T.Q. advocates and a thorny subject for competitors as well as the N.C.A.A. and other sports governing bodies, who are trying to chart a path for athletes who do not fit neatly into the sex classifications used in most sports.

The N.C.A.A. last week amended its decade-old policy for transgender athletes. Transgender women — who are required to be on testosterone-suppressing drugs for 12 months before becoming eligible to compete in women’s divisions — now must meet testosterone thresholds set by the national governing body of the sport they play. The new thresholds could be in place as soon as next month in advance of the N.C.A.A.’s winter championships, which for women’s swimming is in mid-March. (A transgender man may not compete on a women’s team once he has begun taking testosterone.)

The requirement for transgender women comes at a time when governing bodies across many sports are questioning the links between testosterone, which helps young men develop muscle mass through puberty, and athletic performance.

U.S.A. Swimming said on Thursday that it was re-evaluating its policy for transgender athletes at the elite level, meaning the requirements for transgender swimmers could change in the coming weeks.

“Many of the policies are in flux,” said Amy Wilson, the N.C.A.A.’s managing director of inclusion. “It’s a continually evolving space.”

Underpinning the murkiness, Wilson added, is a lack of science to lean on, in part because there are so few transgender athletes among the nearly 500,000 N.C.A.A. athletes. (The N.C.A.A. would not say how many had applied for an exemption to take hormones that are otherwise banned substances.)

While there have been an increasing number of transgender athletes who have transitioned while in college, the ones who generate the most attention (and criticism) are transgender women who compete in women’s events — and who win. Those have been exceedingly rare: for example, Juniper Eastwood, who won running events for the University of Montana, and CeCe Telfer of Franklin Pierce University, who won the 2019 Division II national championship in the 400-meter hurdles.

And now there is Thomas, who has turned in better times this season than several college swimmers who raced in last summer’s Olympics.

Thomas, 22, grew up in Austin, Texas, as an accomplished swimmer. She took to the water about the time she entered kindergarten, eventually finishing sixth in the state high school championships, and followed her older brother to swim at Penn. Thomas gradually emerged as one of the Ivy League’s best swimmers, finishing second in the men’s 500, 1,000 and 1,650 freestyle at the Ivy League championships as a sophomore in 2019.

She did this while also distressed, she said last month in a podcast, telling the swimming website Swimswam that she felt trapped in her own body.

(Thomas has declined almost all other interview requests, including by The New York Times. She plans to tell her story to one outlet, Sports Illustrated. Penn and Harvard officials told reporters Saturday that their swimmers and coaches could not be interviewed.)

Thomas came out to her team in the fall of 2019 and swam intermittently for the men’s team as a junior while undergoing hormone therapy. Then the coronavirus pandemic hit, shutting down all Ivy League sports for a year. She dropped out of Penn last year to preserve her final season of eligibility — the Ivy League at the time did not allow graduate students to compete — and returned to school in August.

It has been “interesting” and “weird,” she said on the podcast, to adjust to a new time standard during training and in races after having dropped so much muscle mass and strength as a result of suppressing testosterone.

For example, her nation-best time in the women’s 500, 4:34.06, is more than 15 seconds slower than her personal best before she started hormone replacement therapy.

“I had a lot of uncertainty about my future in swimming and whether I’d be able to keep swimming at all,” she said of her transition. “I’m just thrilled to be able to swim. I love to compete. And I just love to see how fast I can go. It’s an ongoing evolution of what I think I can go based on how my training progresses and evolves.”

That evolution continued on Saturday, which unfolded quietly.

There were no protesters outside Blodgett Pool at the meet at Harvard, as there had been this month at Penn in Thomas’s final home meet (where there were three police officers present, just in case). And there was no sign of rancor among the crowd, which was restricted to friends and family because of the pandemic. Last month, parents of some Penn swimmers sent a letter to the N.C.A.A. and the university saying that a troubling precedent was being set for all female athletes by letting Thomas compete with the women’s team.

Still, the Ivy League championships lie ahead next month and then the N.C.A.A. championships arrive in March. That will almost assuredly raise the temperature again, as has happened when iconic figures like Michael Phelps, who is making a second career as a mental health advocate, and Martina Navratilova, a champion of L.B.G.T.Q. rights, questioned whether Thomas should compete on a women’s team.

Others, meanwhile, will wonder when the discussion will be centered less on the winner than on the human being.

And so if there was something enduring about Saturday, it was not the two races that Thomas comfortably won or the two relays where she gamely tried. It was the way she carried herself in the water — head down, with grace and ease.