An avalanche of emails, backlogged permits, lapsed contracts and stalled payments to ­low-income Americans will face the hundreds of thousands of federal employees who return to work Monday.

For 35 days, they waited out the shutdown of nine Cabinet agencies and dozens of smaller ones. Now, they’ll face a massive bureaucratic reboot that could take weeks or even months.

The National Park Service will need to restore basic amenities at hundreds of parks and monuments, removing accumulated trash and plowing multiple feet of snow. The Bureau of Indian Affairs must quickly issue grants to head off food shortages and a health-care crisis for Native American tribal members whose funding was cut off.

Inspectors returning from furlough to the National Transportation Safety Board will have to decide which of the almost 100 rail, plane and highway crashes to investigate first. And the Internal Revenue Service will race to train employees to implement changes to the tax code and hire thousands of temporary workers for tax season.

“I’m so ready to go back to work,” said Laura Barmby, an international trade specialist with the Commerce Department. She was so anxious to dig into her backlog she planned to log in to her computer from home on Sunday.

Barmby’s immediate concern is a blown deadline for a prestigious presidential awards program for exporters, “a big deal in my little world,” she said. After that, she intends to contact a group of companies advising the U.S. government on an upcoming trade pact with the United Kingdom to reschedule multiple missed meetings.

Federal workers at the World Central Kitchen food bank in D.C. reacted Jan. 25 to the deal reached to temporarily reopen the government. (Melissa Macaya, Jorge Ribas/The Washington Post)

The first order of business for her and more than 350,000 others who spent the shutdown at home will be simple office tasks, like new passwords for computers. Timecards will need filling out, so payroll staffs know who was furloughed, worked without pay, called in sick, earned overtime or a combination.

Then there will be the reorganizing. After the shutdown was announced in December, agencies had four hours to close. Employees had just enough time to drop off work cellphones and laptops and record voice mail greetings. Many returning workers will find their offices in a holiday time warp. As of Friday, a Christmas tree and Hanukkah menorah still adorned the darkened, fifth-floor reception area of the Merit Systems Protection Board, a personnel court for civil servants in downtown Washington. Vice Chairman Mark Robbins said he’s had no staff to take them down.

New voice-mail greetings will have to be recorded, announcing the reopening. Programs will need to be restarted, a process that can involve many layers of bureaucracy and boxes to be checked. Private contractors may have reassigned employees who had been working on projects put on hold during the shutdown, said David Berteau, president and chief executive of the Professional Services Council, which represents workers at roughly 400 private government contractors.

“It may take days to get started,” he said. “We have no experience at starting back up after five weeks. . . . You have to make sure that the funds are still available before you can start the contract again. And everybody’s going to be trying to do it at once.”

Even employees who are anxious to get back to work say they feel paralyzed by what comes next.

When she steps into her office at NASA’s Goddard Space Flight Center on Monday morning, astrophysicist Julie McEnery knows exactly what she’ll do first: water her plants. But then?

“I’m scared to even think about it,” she said. “The amount of work isn’t less, and we’ve got a lot less time now to do it.”

As project scientist for the Fermi Space Telescope, which surveys the cosmos using the highest-energy form of light, McEnery was called into Goddard a couple of times this month to take care of specific tasks related to the maintenance of the telescope. “I hope people know this was not a vacation,” she said. “It was very discouraging. . . . We’re not all going to arrive back at work Monday bright-eyed and bushy-tailed.”

To boost morale, several agencies are planning hero’s welcomes for their staffs. The Peace Corps is holding an official event for returning employees starting at 7:30 a.m. Monday.

But many workers say they’re still anxious. They won’t see the back pay they’re owed until later this week. And President Trump has threatened another closure in three weeks if his demands for border wall funding aren’t met.

“It’s a reprieve,” said Gary Morton, president of AFGE Council 238, a union representing about 9,000 Environmental Protection Agency employees around the country, “but how much will we be able to accomplish before we have to start worrying about shutdown procedures again if they don’t reach a deal?”

Several federal managers said their agencies still cannot issue or announce new grants with the uncertainty of such a short-term budget. A senior manager at Homeland Security who spoke on the condition of anonymity because he is not allowed to speak publicly said he is allowing his staff to work from home until they have back pay cash in hand.

For offices in which staffs were essentially entirely furloughed, the return to normal operations could be particularly slow.

The EPA, for example, must update its enforcement actions database, which has sat idle for more than a month, along with other key computer registries and air and water permits across the country, a senior administration official said. Agency experts had stopped certifying that new auto models meet U.S. air standards, slowing Fiat Chrysler’s plan to bring in a new model of a heavy-duty commercial work truck, officials said.

The Food and Drug Administration will start taking new drug and medical device applications, but agency officials acknowledge they may not fully catch up for almost a year.

Then there will be the physical messes to clean up.

At Mount Rainier National Park in Washington state, where no snow has been plowed since before Christmas, staffers must clear a highway stretching several miles uphill 2,500 feet in elevation to the main visitor center, along with large parking lot now covered by at least three feet of snow, with seven-foot drifts. Park officials announced Saturday that visitors should be able to reach Longmire, where the park’s hotel and museum are located, Sunday. But they cautioned it “may take many days” to restore access to the main visitor center and other high-elevation attractions.

A major cleanup awaits the staff at Sagamore Hill National Historic Site in New York, where a fire started in the gift shop late last month. On Monday, Park Service staff will continue working through the damage to document what has been lost and begin cleaning up.

The IRS told lawmakers last week that the agency will be buried in millions of unanswered taxpayer letters, weeks behind schedule on training and short thousands of new employees for this tax season, according to two House aides who were not authorized to speak publicly about the matter.

The National Taxpayer Advocate Service, a government watchdog group that oversees the tax collector, told House staffers it will likely take a year for the IRS to run normally again, the aides said.

The reopening of the Smithsonian scheduled for Tuesday will mean much more than the return of visitors. Deadlines for upcoming exhibitions have passed. The National Gallery of Art has been unable to prepare for its much-anticipated Tintoretto show, set to open March 10. It’s the highlight of its spring calendar — the first North American retrospective of the Venetian artist — and the staff is worried about a potential delay.

Three other exhibitions have been postponed because work on the installations couldn’t be done: “Votes for Women: A Portrait of Persistence” at the National Portrait Gallery (set to open March 1) “Striking Iron: The Art of African Blacksmiths” at the National Museum of African Art (Feb. 27) and the Smithsonian Gardens’ popular orchid display, planned this year for the Kogod Courtyard at the NPG and Smithsonian American Art Museum. (Feb. 2). New opening dates have not been announced.

Federally funded science research could take a long time to recover too, scientists said. At the National Science Foundation (NSF), there’s a backlog of nearly 2,000 research grants waiting to be reviewed, on subjects ranging from cyberinfrastructure to earth sciences. More than 100 panels of outside scientists were canceled during the shutdown. Rescheduling them will be a massive undertaking.

“The impacts are going take some time to sort out,” said Benjamin Corb, spokesman for the American Society for Biochemistry and Molecular Biology. “It is likely that the scientific enterprise won’t truly know what the impact was for months.”

A program director for the NSF, who spoke on the condition of anonymity to speak frankly, said the agency’s reopening brings much uncertainty.

“It doesn’t feel resolved at all,” the program director said. “I’ll be very happy to see my colleagues and make a little progress. But it’s not like we feel relieved. We worry that we’re just going to be used again in three weeks, if nothing is resolved.”

Work also has piled up in the Bureau of Prisons. All but 3 percent of employees were required to report to work, but those returning Monday have mixed feelings.

In the Equal Employment Opportunity Commission office, where employees file harassment and discrimination cases complaints, one counselor said 150 to 200 cases will be waiting when they return.

“It’s going to be crazy,” the counselor said, speaking on the condition of anonymity because they did not have permission to speak with the media. “I expect to have at least 300 emails waiting for me. The cases may have been placed on hold, but the harassment has been allowed to continue while we were gone.”

At Coleman penitentiary in Florida, Joe Rojas, union president, said several employees quit during the shutdown, including a secretary hired days before it began.

“There is a lot of work piled up on his desk that someone is going to have to handle,” Rojas said. “When you start a job, you don’t expect them to say, ‘By the way, we aren’t going to pay you for this.’ ”

Joel Achenbach, Carolyn Johnson, Peggy McGlone, Brady Dennis, Kimberly Kindy, Laurie McGinley, Dan Lamothe and Amy Goldstein contributed to this story.