By now, readers have undoubtedly heard about the tens of thousands of children streaming over the border, largely from Guatemala, El Salvador, and Honduras. The ranks of unaccompanied children, as they are known, has grown dramatically in recent months as children flee some of the most dangerous countries in the world outside of active war zones in hope of finding safety and refuge away from the gang violence and murder in their hometowns. Secretary of Homeland Security Jeh Johnson predicted a few weeks ago that their numbers would reach 90,000 by the end of the fiscal year on September 30, most of whom are expected to be from Central America.

By the middle of next month, the federal government could run out of money for detaining and deporting them. The president has requested $3.7 billion in emergency funds to carry federal agencies through the end of fiscal year 2014. Whether Congress will return to Washington, D.C. for a vote on the bill before the federal government runs out of money isn’t clear yet. But one thing is becoming clear: Immigration may not be the only policy affected by the influx of these children. Education funding could feel ripple effects, too.

Under federal law, the Department of Health & Human Services (HHS) is responsible for placing and caring for unaccompanied children through its Office of Refugee Resettlement, rather than Immigration and Customs Enforcement or another office. But usually, HHS serves about 7,000 to 8,000 children a year — until fiscal year 2012, when it jumped up to 13,600, and then increased again to more than 24,600 in 2013. HHS uses these funds to provide the kids a baseline of safety, health, and education. But doing right by these children isn’t cheap. Of the $3.7 billion emergency request the White House made earlier this month to deal with the situation, $1.8 billion would be earmarked for HHS to care for the children.

But the funding typically isn’t augmented by emergency funding — it’s folded into the agency’s annual budget. In fiscal year 2014, Congress enacted funding totaling $868 million for unaccompanied alien children, up from $376 million just one year prior. And that funding doesn’t even include the emergency dollars, so as the numbers of children keep growing, next year’s regular budget will likely need to be even larger.

That’s where the trouble starts for education spending. In 2011, Congress passed the Budget Control Act (BCA), implementing a series of spending caps to limit federal appropriations funding over the next decade. Under the BCA regime, funding is zero-sum, because absent congressional action (like lifting or removing the caps), the limits hold for all appropriations. So once the HHS funding for unaccompanied children is wrapped into the regular appropriations–rather than counted as emergency funding, which isn’t subject to the spending caps–every dollar directed to that cause will be counted against the overall appropriations limit. And since the Departments of Labor, HHS, and Education are all funded in one package by Congress, the trade-offs in funding will likely come from within those agencies. If the problem continues to grow, funding for the immigration crisis could eat into the federal budget for education programs.

And there’s another political concern, even beyond Congress’s spending caps. As the unaccompanied minors debate is heating up, members of Congress are taking sides. A number of Republicans in Congress have vehemently opposed the Obama administration’s recent detention efforts for the children, arguing they aren’t coupled with strong enough border security and deportation efforts. Given the delays and pushback the administration has already seen on its emergency funding request, it seems possible, if not likely, that it won’t be the last time lawmakers hesitate to write a check. As Congress prepares to produce and pass fiscal year 2015 spending bills (albeit something that will likely happen after the deadline passes on September 30, 2014), the unaccompanied children funding could likely be on the list of reasons lawmakers choose to hold off on approving new spending.

Lawmakers are now dealing with a humanitarian crisis: tens of thousands of unaccompanied children traveling to the U.S. to escape violent, poverty-stricken countries. But now that the crisis is in full swing, lawmakers have to decide whether they want to stand by the arbitrarily determined, sometimes-painful spending limits in place now, or whether they should revise the budgetary policy to fit these exceptional circumstances. The choice is theirs.

[Cross-posted at Ed Central]

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Clare McCann is a policy analyst with the Education Policy Program at the New America Foundation. Find her on Twitter: @claremccann