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For weeks, legislative leaders have been unable to reach a compromise to close the books on last fiscal year, leaving a relatively routine spending bill and a $1.1 billion surplus that it is built on to languish.

But that impasse is affecting more than just the state’s ledger: Hundreds of millions of dollars that the policy-heavy legislation promises also remains in limbo, affecting everything from the MBTA and school security to helping ensure that public water supplies are safe.

The delay is prompting rounds of hand-wringing and calendar-watching among advocates and agencies, who are left to wonder not just when, but in what shape, a bill could emerge before Dec. 11, when the state comptroller said he intends to close the books himself.

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“It’s mind-boggling to me that this did not pass,” said Kyla Bennett, the director for Public Employees for Environmental Responsibility in New England, which has advocated for $28.4 million that both the House and Senate bills allocate to test for and address “forever chemicals” — per- and polyfluoroalkyl chemicals known as PFAS — in town water supplies.

“This delay is forcing all of us at the customer level to buy filtration systems and worry,” she said. “It’s a national crisis. I thought Massachusetts was on top of it, but apparently not as much as I thought.”

Known as a supplemental budget, the legislation is designed to formally wrap up the fiscal year that ended on June 30, while pushing a deposit into the state’s rainy day fund and parsing out money to various accounts and programs.

But the House and Senate, which have struggled for years to finish their annual budget negotiations without delays, have been unable to reach a compromise more than a month after both chambers passed their own versions of the supplemental bill.

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The legislation differs on a wide range of fronts, with the Senate version adding tens of millions of dollars more in appropriations and eliminating a corporate tax change that the House backed, among other things.

Even on pots of money where there’s broad agreement, the two chambers don’t always see eye to eye on the specifics.

The legislation, for example, includes $50 million for the Massachusetts Bay Transportation Authority, an agency that House Speaker Robert A. DeLeo once dubbed in “crisis.” It’s an infusion that Governor Charlie Baker has called for since June to fund a new team of engineers, maintenance workers, and contractors to speed projects and repairs. But unlike the House, the Senate also requires the agency to produce reports updating the progress of its capital projects as part of receiving the funding.

Lisa Battiston, an MBTA spokeswoman, said planned projects are still moving forward but the funding would help the agency do more proactive inspections and maintenance.

The T — which this year has been battered by high-profile service disruptions and frustration over fare hikes — would also add contracts “to focus on accelerating construction and infrastructure projects” if the funding is approved, Battiston said.

The bills include closely watched policy proposals, as well, such as a much-debated decision to move the state primary date next year to Sept. 1. It also features language that DeLeo said would ratify several collective bargaining contracts, including with unions representing community college staff and registry of deeds workers.

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In a letter Monday, DeLeo floated the idea of passing a bill that strips out discretionary spending and includes only funding to shore up deficient “budgeted accounts” and time-sensitive policy proposals, such as setting the primary date.

But it’s unclear if there’s an appetite elsewhere for such a move. A spokesman for Baker’s budget office, which DeLeo asked to produce a list of accounts with deficiencies, said Friday it’s still reviewing DeLeo’s letter.

A spokesman for Senator Michael J. Rodrigues, the chamber’s budget chairman, said he was unable to reach the Westport Democrat on Friday.

“There’s a lot of priorities for many of us in both versions of the supplemental budget, in the House and the Senate,” said Representative Aaron Michlewitz, the chairman of the House Ways and Means Committee. “I’m hopeful, and continue to be eager to come to a resolution on this that can move the ball forward.”

Meanwhile, loads of earmarks hang in the wind. The legislation sets aside millions for grants to help schools beef up security, including for installing new door locks, security cameras, or active-shooter detection systems. Both versions also would push an additional $1 million into a nonprofit grant program designed to help houses of worship and other organizations add new security measures.

Aaron Agulnek — director of government affairs for the Jewish Community Relations Council of Greater Boston, which publicizes the nonprofit grants’ availability to local centers and synagogues — said the grant process is moving forward as expected after the program received $500,000 in the current state budget. But the delay has left unclear exactly how many applicants could ultimately benefit.

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“The fact remains, it’s unfortunate that with so many areas of consensus . . . which real people and real priorities are impacted by, that [lawmakers] haven’t been able to move forward,” Agulnek said of the budget bill.

To others, the stalemate is now in uncharted territory. Andrew W. Maylor, the state’s comptroller, told lawmakers in a Nov. 21 letter that absent a budget deal, he will unilaterally close the fiscal year 2019 books on Dec. 11 and transfer the surplus into the state’s rainy day fund.

That would mean the funding that legislators had hoped to put toward the various programs and earmarks would instead go into the state’s emergency savings account.

Maylor said he’s staring down deadlines to file the state’s comprehensive annual financial report and send information to federal officials that affects billions of dollars that the state receives each year in federal funds.

“I must emphasize that the Commonwealth is in an unprecedented situation,” he said.

It’s also about to become an awkward one. Even as they figure out a way to finalize spending from last fiscal year, lawmakers will begin a new process Wednesday: trying to reach agreement on what tax revenues will look like in the next one.


Matt Stout can be reached at matt.stout@globe.com.

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