Which specific programs within the remaining CR‑covered appropriations are most likely to face furloughs or grant pauses if funding lapses?
Executive summary
A lapse after the continuing resolution (CR) that covers nine of the 12 regular FY2026 appropriations would force appropriated, discretionary programs to “cease or scale back” immediately and could trigger furloughs for non‑essential employees in those agencies, while mandatory payments keep flowing into March 2026 per the CR’s language [1] [2]. Programs most at risk are the familiar slate of discretionary grant‑heavy public‑health, environmental, housing, and homeland‑security accounts that the CR explicitly continued only through January 30, 2026 — notably CDC, HRSA, SAMHSA, EPA, and various Transportation‑HUD and Homeland Security activities [3] [4] [5].
1. Which buckets are actually on the chopping block: discretionary, grant‑heavy accounts
The CR provided temporary funding for most agencies through January 30, 2026, but it does not change the basic rule: appropriated discretionary programs — about one quarter of federal activity — stop or scale back when appropriations lapse, making grant programs and operational accounts funded annually the most exposed [2] [1]. The CR’s text and implementing guidance also instruct agencies to limit spending during the CR and to avoid “new starts,” which means existing discretionary grants and grant solicitations are the obvious candidates for suspension if funding ends [6] [7].
2. Public health grants: CDC, HRSA, SAMHSA — first in line for pauses
State and local public‑health grants administered by the Centers for Disease Control and Prevention (CDC), Health Resources and Services Administration (HRSA), and the Substance Abuse and Mental Health Services Administration (SAMHSA) are explicitly covered by the CR and have historically been curtailed or paused during lapses because they depend on annual appropriations and often require continuing apportionments to pay out awards — the CR keeps current levels only through Jan. 30 [3] [2]. The CR also contains provisions specifically aimed at slowing grant outlays during the interim period to preserve congressional prerogatives, which heightens the likelihood of pauses in grant competitions, awards, and formula disbursements if the CR expires [7].
3. EPA, Transportation‑HUD and other domestic programs that depend on discretionary appropriations
Environmental programs and grants at EPA, community development block grants and HUD formula/competitive programs, and Transportation‑HUD accounts are funded annually and were included under the CR’s coverage; these accounts are therefore vulnerable to immediate reductions in activity or halted grant payments if another lapse occurs beginning January 31 [3] [4]. The CR’s instructions to apportion conservatively and prevent new activities mean capital planning, discretionary grant competitions, and new contract initiations at these agencies are likely to be frozen or delayed [7].
4. Homeland Security and enforcement functions: furlough risk and political pressure points
DHS and immigration‑related agencies are a central political sticking point and are funded under the remaining CR framework; a funding lapse could quickly produce furloughs among non‑essential staff and curtail routine functions, even as some enforcement activities may be excepted by law, creating uneven operational impacts [5] [1]. The reporting shows DHS funding was a negotiation pivot this year and, historically, partisan battles over DHS funding increase the odds that components funded by the CR would see rapid workforce disruptions if appropriations lapse [5].
5. Mitigating factors and likely exceptions — what might keep running
Two important caveats reduce the universe of programs that will stop entirely: mandatory payments covered by the CR continue into March 2026, and agencies can sometimes rely on prior‑year obligations, multiyear contracts, or statutory exceptions to sustain certain operations temporarily — examples documented in prior shutdowns and discussed in contingency guidance [2] [8]. That said, the CR’s own riders to “prevent spending money too quickly” and to bar new starts make discretionary grant awards and solicitations the most predictable casualties of a lapse [7].
Bottom line: the most likely furloughs and pauses
If the CR expires, the first and clearest impacts will fall on annual discretionary, grant‑dependent programs such as CDC/HRSA/SAMHSA public‑health grants, EPA environmental grants, Transportation‑HUD housing and community grants, and many DHS operational functions; these accounts are covered by the CR only through Jan. 30 and are structured so that a lapse forces agencies to stop or scale back appropriated activities and, in many cases, furlough non‑essential staff [3] [4] [1]. Where statutory exceptions or carryover funding exist, operations may continue in part, but the CR’s own constraints on new spending and apportionment amplify the chance that new grants, open competitions, and discretionary program starts will be paused until lawmakers act [7] [8].