Impacts to Federal Science Under the Shutdown: A Review
In the early morning hours of October 1st, the long anticipated government shutdown cast its shadow across the nation. Every year, Congress, which has the power of the purse, must pass funding bills for the new fiscal year, which begins on October 1st. When Congress fails to pass either full-year appropriations or short-term continuing resolutions, funding lapses and agencies can’t legally spend money, triggering a shutdown. During a shutdown, many federal employees are furloughed - temporarily unpaid and barred from working - while personnel deemed “excepted” continue working without pay until the lapse ends.
This results in halted prevention, research, oversight, reporting, and planning - the quiet daily work that keeps Americans safe and healthy - until funding resumes. While many outlets have cataloged both the historical impacts of government shutdowns and specific anticipated agency-by-agency consequences, we focus here on cross-agency federal science and research capacity.
Federal Research Capacity - Broad Trends
Broadly speaking, across health/science agencies, research programs and day-to-day processes that keep federal research processes running are paused. For example, NIH can’t run grant peer review, meaning promising biomedical research is stalled for months or longer in anticipation of funding. The CDC slows the public health program guidance that clinicians and schools use to make real-time decisions. USDA research pauses - delaying crop, livestock, and food-safety studies that stabilize prices and protect supply chains. EPA research and many inspections have halted, leaving polluted air and water unchecked and allowing risks to go unnoticed. FEMA data collection across climate-relevant agencies pauses, pushing outdated flood and wildfire risk information into the maps that shape insurance rates, building codes, and evacuation planning. In the last prolonged shutdown, (2018-2019), additional documented effects include: halted NSF grant flow, NOAA research stoppages, and suspended EPA inspections.
The long-term cost is steep, including delayed treatments, higher long-term cleanup and healthcare costs when problems aren’t caught early, lost continuity in datasets that scientists cannot reproduce, and a potential talent drain as researchers ride out funding gaps that they cannot afford.
The Department of Health and Human Services
The department of Health and Human Services plans on furloughing ~41% of its workforce on average; NIH expected to furlough >75% of its workforce, CDC 64% of its staff, CMS 47%. Additionally, CDC communications and guidance slow down, delaying outbreak alerts and best-practice guidance for clinicians and schools. The NIH will be unable to admit new patients to their Clinical Center, and grant peer review/advisory meetings will stop. Clinical research is expected to be ‘upended’ at the NIH. Current trial participants will be able to continue care, but NIH will pause most new clinical studies - freezing potentially life-saving research.
Although the FDA is maintaining most of its staff, it nonetheless expects its ability to protect/promote public health will be ‘significantly impacted’, including delays or pauses for activities such as accepting new drug/device submissions. Medicaid/Medicare benefits to current beneficiaries are expected to continue if the shutdown is brief. A more prolonged shutdown, however, is likely to delay provider payments as administrator funds deplete.
The Environmental Protection Agency (EPA)
When nearly 90% of EPA staff are furloughed, the country’s early-warning system for dirty air and unsafe water goes dark. Routine inspections at hazardous-waste sites, drinking-water systems, and chemical facilities pause - meaning small problems can snowball into community-level exposures before anyone official is there to catch it. Research and permitting also stall, leaving towns and businesses in limbo on projects that require air and water safeguards to move forward. Additionally, enforcement to ensure facilities follow environmental laws and permits largely freezes, which suspends deterrents that keep bad actors from cutting corners in the first place.
Past shutdowns set a precedent: EPA inspections have previously been suspended, and Superfund cleaning operations have been delayed or halted in the past. A shutdown also compounds earlier 2025 cuts/reductions in force that already weakened EPA capacity, heightening risks to air/water oversight until these staff return to the office.
The Federal Emergency Management Agency (FEMA)
Government shutdowns halt data collection and research at climate and emergency-management agencies like FEMA, eroding preparedness and leaving state and local planners without the information they need to respond to future disasters. We as a nation lose flood maps, fire-risk models, and storm-surge forecasts that counties use to set building codes, plan evacuations, and decide what infrastructure needs upgrades first. Additionally, delays to long-term mitigation projects - like elevating structures and shoring up levees - hampers lifesaving work and makes future disasters costlier.
It is expected that about 4,000 FEMA employees will be furloughed, according to the agency - meaning the analysts, engineers, and planners who turn raw climate data into usable risk guidance are thinned out. This in turn means states and towns get slower updates and fewer technical consults, just as they’re budgeting for the next season. While active firefighting operations are expected to continue, a shutdown could stall forest management and fire prevention projects. The timing is especially concerning, as this year’s fire season has been mild - leaving more unburned vegetation. This results in a greater need for prevention and resilience work that could now be delayed.
The U.S. Department of Agriculture (USDA)
Pauses at USDA will include ongoing research, reports, outreach/technical assistance, many regulatory activities, hazardous fuel treatments, special-use permits. About half of USDA’s employees (more than 42,000) are expected to be furloughed. Many county service centers will close or run with skeleton crews, so payment processing and disaster assistance stop, and producers lose time they can’t afford during planting or harvest. Pauses with USDA research and market reports mean fewer reports and less technical assistance, leading to both producers and consumers facing more uncertainty at the grocery store.
Within the Farm Service Agency (FSA), roughly 67% of employees will be furloughed. In the Food and Nutrition Service (FNS) most staff will be furloughed, although a select few will remain on to administer SNAP (food assistance), child nutrition programs, and WIC (nutrition for pregnant/postpartum people and young children). The Forest Service will retain ~20,000 of 32,390 employees to handle wildfire, land protection, and other mission-critical tasks, although public recreation access may be curtailed.
So, What Does It All Mean?
This shutdown isn’t over minor disagreements. GOP leaders are holding the government and its services hostage to push their agenda, which includes rejecting the extention of enhanced ACA premium subsidies - the extra help that keeps marketplace insurance affordable - pushing us into this painful lapse that pauses research, inspections, and prevention. These standoffs are ideological wagers over what the government should do, and who it should protect. Yes, government shutdowns carry heavy consequences for the health of our nation - but abandoning this fight could cost us even more. We’re in a lose-lose scenario.
At Stand Up for Science, we believe the government has a responsibility to provide science-backed services that uphold the life, liberty, and well-being of all Americans. When lifesaving programs are held hostage, we look beyond the gridlock to a different remedy beyond negotiations: elections.
Thus, we refuse to simply mourn the shutdown. At Stand Up for Science, we’re fighting against those who gamble with public health and wellbeing to advance their agenda - and we need your help. We recently launched the Science Fight Club - and there are only two rules:
Only a Congress without accomplices stops Trump.
Once we take back Congress, we disband the Science Fight Club.