In many respects, these are heady days for Nautilus, the highbrow science and culture magazine launched precisely four years ago this weekend. Traffic to its original website is setting records, its print edition has been well-received, and in its short existence, the magazine has earned numerous awards for its design and its journalism, including two National Magazine Awards — arguably, the industry’s highest honor.

More recently, it drew laurels for an essay by Cormac McCarthy — the first piece of nonfiction that the legendary novelist has ever published — and the magazine’s publisher has suggested that a major new partnership with a science organization is in the works.

For all the good news and accolades, however, murmurings within the science writing community suggest that not all is well at Nautilus. Rumors of delayed or entirely absent payments to the magazine’s fleet of freelance contributors have reached a crescendo, as have complaints that editorial staff continue to solicit work knowing that the publication may not be able to make good on promised fees.

One Nautilus freelancer, who asked to remain anonymous because thousands of dollars in fees are still pending, received a note a few months ago directly from the magazine’s publisher and editorial director, John Steele, offering assurances that the funds — which were for a feature that the magazine published last year — would be on their way by the end of January. That deadline came and went without payment, the freelancer said, and follow-up emails to Nautilus have not changed things.

“It’s sad,” the writer said, “because we need science publications that pay decently — if they actually pay.”

Linda Marsa, a Los Angeles-based journalist, had more success. Marsa wrote a piece last fall, submitted an invoice, and didn’t get paid on time. On Facebook, she learned that other writers were experiencing problems too. Frustrated, Marsa sent what she describes as a “stern” email to her editor, as well as the finance manager, the publisher, and a member of the Nautilus board.

That worked, and her payment arrived roughly a month overdue. When I called Marsa, she was surprised and upset to learn that the problems were continuing. Describing her editor at the magazine as “a gem,” Marsa said she’s nonetheless disillusioned and does not plan to write for the magazine again. “I’m really sad I’m not going to get to work with him again,” she said of her editor, “but this isn’t right.”

The publication’s exquisitely designed web site and print edition don’t come cheaply, and staff have taken pay cuts.

In a phone call with Undark, Steele, the Nautilus publisher, acknowledged that the magazine “has been running on fumes for the past six months,” and that it was behind on payment for many of its writers and illustrators. “We feel horrible about the way the situation has dragged on so far,” he said. “It tears me apart that I can’t fulfill these commitments that I’ve made to these guys, when they’ve given us such fantastic work. But I say, ‘Look, you’re going to get it. It’s going to happen. Just bear with me a little while longer.’”

Steele, a former television journalist, started Nautilus in 2012 with a two-year, $5 million grant from the John Templeton Foundation, a Pennsylvania-based philanthropy that describes itself as targeting the world’s “big questions” in science, religion, and philosophy. That money, supplemented with an additional $2.1 million from Templeton, was the main funding source for Nautilus in the run-up to publication, and during its first two years in print. But the Templeton Foundation typically reduces support for startup ventures after the first three years, and, accordingly, it has dialed back funding for Nautilus, although it gave the magazine an additional $1.25 million in 2015, and a little more than $1.2 million last year.

“It’s simply a matter of our desire to step back and not be a sustaining funder for the indefinite future, but rather allow [Nautilus] to grow and flourish,” said Christopher Levenick, the director of public engagement for the Templeton Foundation. He said he was unaware that Nautilus has been experiencing cash flow problems and failing to pay contributors.

Steele’s continued confidence that the magazine’s money problems will be short-lived is rooted in what he describes as the publication’s pending absorption by the American Association for the Advancement of Science — the world’s largest general scientific organization. The talks with AAAS began in December, Steele told me, after months of hunting for a new institutional home. The publication has also lined up funders who would step in and add additional resources once the deal with AAAS is complete. In principle, Nautilus would become a part of AAAS, and the funders will help put Nautilus in the black until it becomes profitable on its own, Steele added — though he declined to name the additional funders because the details have not been finalized.

Steele said he thought the arrangement with AAAS would proceed quickly, which is why he felt comfortable commissioning new work and telling freelancers that their money was on the way. But that didn’t happen. The process of coordinating among the funders and AAAS has moved slowly, and Steele told me that the magazine stopped commissioning new articles in late February or early March, once it became clear that they would not finalize the AAAS deal and have new funding as soon as he had anticipated.

Tiffany Lohwater, a spokeswoman at AAAS, did not respond to Undark’s request to discuss Nautilus over the phone, saying only in an email message that “Nautilus approached AAAS to inquire about the possibility of an affiliation, and AAAS is in the process of exploring that.” When pressed, she added: “AAAS is very much in the exploratory stage of any potential affiliation. There is no arrangement.”

That disconnect suggests, at the very least, that the lean times will continue — both for Nautilus, and for its unpaid contributors. Over the last several months, the magazine has gradually shrunk the size of its budget, and all staff have taken pay reductions. Today it earns revenue through individual donations and grants from other foundations; from subscriptions to its digital and print products (the latter is currently published in partnership with MIT Press); and, more recently, from branded, foundation-sponsored verticals, called channels, that are each devoted to a specific theme.

Steele says he intends to begin offering more writers partial payments beginning next month, drawing on revenue from Nautilus subscribers and sponsors. Asked whether Nautilus pays writers interest on their overdue fees, Steele said that he does so “on an individual basis” and when people specifically ask for additional compensation.

That might be welcome news for some writers, for whom even a single delayed payment can sometimes be financially disastrous. One contributor, who did not want to be named in order to preserve a working relationship with the magazine, told me that delayed payments from Nautilus had made it hard to pay the bills.

“I started pitching other places,” the freelancer said. “And I started dog walking.”