Some agencies, like the E.P.A., have been virtually shuttered. Almost 95 percent of the agency's 16,000 workers have been told to stay home. And while some longtime opponents of environmental regulation cheer that temporary outcome, others are deploring what could be lasting impacts on the environment.
"It is a polluter's heyday," said Sara Chieffo, the legislative director of the League of Conservation Voters. Normally, she said, "they are doing the inspections that need to be done, making sure that polluters are held to account."
"We know that the longer this goes on, the cascading effects occur," she added.
Dan Ronnenberg, who is on a furlough along with thousands of other safety inspectors for the Federal Aviation Administration, said tasks not being performed included inspections of the de-icing of aircraft on the tarmac and checks that pilots do not fly longer than allowed. He said the risks to flight safety increase the longer outside inspectors were off duty.
The shutdown initially sent about 800,000 workers home on Oct 1. The Defense Department recalled most of its 350,000 civilian work force, and others who are deemed essential have returned piecemeal, like thousands of C.I.A. employees and experts at the Centers for Disease Control and Prevention needed to confront a salmonella outbreak.
Agreements were reached between the federal government and states to reopen a number of national parks and monuments, including the Statue of Liberty, Grand Canyon National Park, Mount Rushmore and parks in Utah and Colorado.
But the shutdown has left close to 500,000 employees still on furlough, according to the American Federation of Government Employees.
The House passed a bill to assure that they receive back pay, which the White House supports. Even if workers are financially made whole, their uncertainty about whether another shutdown could occur was giving many pause about making big purchases.
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Andrew Sailes, a mechanic at Bolling Air Force Base in Washington, and his wife have put off buying a house for a year. "We've got to sit in our apartment until we get some more money," he said. "We had to push everything back."
The furlough comes on top of the all-agency spending cuts earlier this year known as sequestration, which forced some workers to take unpaid leave and departments to cut budgets. Republicans applauded reducing the size of the government, but some economists calculated that the cuts have slowed the nation's growth.
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Scientists said that one of the most serious casualties might be the country's reputation. Markus Kissler-Patig, the director of the Gemini Observatory, an international coalition with telescopes in Hawaii and Chile, said he was worried about the United States' foreign partners if the coalition's cash flow, which is administered by the National Science Foundation, were to run out. The foundation, which is almost entirely furloughed, cannot provide cash infusions during the shutdown.
"I am starting to hear informal feedback questioning whether the N.S.F. is the right agency to run this international observatory," he said.
Nor could the timing have been worse for the James Webb Space Telescope, an $8 billion contraption that unfolds like an origami figure in space and will be capable of detecting the universe's earliest galaxies.
Scientists have toiled for years and were poised to put its inner workings to the test by simulating the vacuum of outer space in a structure the size of a grain silo when the shutdown halted work at the NASA-run facility in suburban Maryland.
"It's just sitting there twiddling its thumbs," said Matt Mountain, the director of NASA's Space Telescope Science Institute.
Also suspended was work at the South Pole, which involves collecting information critical to studying climate change and can be done only a few months a year. "In my whole career, this is the most frustrating thing I've ever seen," said Ross Powell, a geologist who has been going to the South Pole since the early 1970s.
At the E.P.A., officials have allowed about 900 employees to stay on the job, responding to imminent threats to the environment or to public health. Workers are reporting for duty at toxic waste sites that pose a direct threat to surrounding communities.
But officials said the bulk of the agency's work had been suspended. Industrial chemicals are not being screened for potential health effects. Routine inspections of drinking water systems across the country have been halted.
Some of the agency's critics say the work stoppages are proof of what they have contended for years: that the agency's efforts to issue environmental rules reach too far into American life and should be curtailed.
"There is some good news out of the shutdown," Representative Marsha Blackburn, Republican of Tennessee, wrote on Twitter. "The E.P.A. can't issue new regulations."
But supporters of the agency said the shutdown had affected critical tasks related to keeping the nation's air and water clean. Representative Lamar Smith, Republican of Texas and chairman of the House Science, Space and Technology Committee, said he hoped the shutdown would end soon.
"The partial government shutdown has delayed investigations and ongoing scientific studies at the agency," Mr. Smith said.
But the E.P.A.'s shutdown has also created economic effects as the agency has stopped certifying certain products that enter the country for sale. Among those is millions of dollars' worth of chemicals used to make pesticides. They are stuck in customs because E.P.A. field workers are not available to review and approve them.
At the nation's ports, some cars and trucks are stuck in limbo because there are no E.P.A. inspectors to certify the emissions stickers that are put on the windows.
Anne Lucas, a chemist for the Food and Drug Administration in Maryland who has been on furlough, said she was not worried about her finances but was unhappy to be idle so long. "We all just want to get back to work," she said. "Most federal workers are not there for the money, they're there for the service."
She has been volunteering at a nature center, where she is assigned to pick up trash, a task she said was preferable to doing nothing. "Just because I have a Ph.D. doesn't mean I'm too good to pick up trash," she said.
Matthew L. Wald contributed reporting.