The episode is also a live-action civics lesson, demonstrating how a small but determined interest group can work the levers of government to its advantage.

At issue are fees to help fund several massive tunnels being built beneath the nation’s capital to divert storm-water debris and sewage from the Anacostia and Potomac rivers — once among the nation’s most polluted waterways — and Rock Creek. The project was required under a 2005 federal consent decree.

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The District’s water utility board is now considering a $4 million relief package for nonprofit groups that say they’re unfairly burdened by the payments — with special treatment for religious organizations. Houses of worship would face much easier eligibility requirements than other nonprofit groups to get the grants.

That has outraged critics, who say the District is bestowing a windfall on churches that are already exempt from most taxes. Some say the plan could violate the First Amendment’s establishment clause, which limits government actions that unduly favor religion.

“You do this, and you’re subjecting yourself to the potential for a federal constitutional lawsuit,” said Alan Roth, a District resident and former member of the water utility’s board. The city’s ­churches, he said, “saw it as a great opportunity to pick the taxpayer’s pocket.”

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Church leaders are also unhappy — that they’re not getting more money.

The Rev. Willie Wilson, pastor at Union Temple Baptist Church in Anacostia, said the city’s package of fee breaks “doesn’t begin to address the problem in terms of the kind of stress and strain it’s putting on churches.”

Wilson said churches such as his own were especially vulnerable; in recent years, he said, his predominantly African American congregation has dwindled as longtime Washingtonians have been displaced by rising housing costs, leaving the church with less financial support.

“It is definitely an issue of race,” Wilson said. “Gentrification has certainly played a role in it, looking at it from a much more comprehensive perspective.”

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Craig Muckle, public policy manager for the Archdiocese of Washington, said the discounts that churches would theoretically be entitled to — which would reduce their fees by up to 90 percent — are generous. However, he said the amount of taxpayer money the city is setting aside in its relief fund, about $3.85 million, is “woefully inadequate” and could soon run out. That could leave financially strapped churches unable to fulfill their mission to help those in need, he said.

“The faith community at large is the safety net on social services for the city government,” Muckle said. “Without the faith community, many of the social services that are offered can go away.”

Tommy Wells, chairman of the D.C. Water board and director of the city’s Department of Energy and Environment — which drafted the proposed relief package — noted that low-income residents, as well as nonprofit groups and churches, would get added breaks from fees under the proposal. The residential discounts would be worth about $8 million, a D.C. Water spokesman said.

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Wells said he did not believe that the District was risking a lawsuit over the establishment clause, arguing the policy did not favor any specific religion over others and was not different in principle from churches’ tax exemptions. He said city officials were doing their best to create an equitable system.

“We’ve thought a lot about that in trying to get this right,” he said.

The board is scheduled to vote on the new policy at a Dec. 6 meeting. If approved, the utility would begin accepting applications for fee discounts in January.

The dispute began with what seemed a simple enough case of a government policy’s unintended consequences. The fees that D.C. Water customers began paying toward the river project in 2009 are calculated based on how much of a property is made up of hard surfaces that don’t absorb rainfall. In theory, that means ratepayers whose land generates more runoff during storms would bear more of the cleanup burden.

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Cemeteries, whose large plots often include a network of roads and flat, stone memorial markers, soon noticed that their bills were soaring.

The new fees were “frankly a little devastating to us,” said Paul Williams, president of the nonprofit that runs Congressional Cemetery in Hill East.

“When I started here six years ago, our water bill was $300 a month,” he said. “Now it’s crept up to almost $3,500 a month, with no increase in water usage.”

News reports on such complaints appeared toward the end of 2017. But if the impact of fees levied from cemeteries was unforeseen, so was what happened next.

D.C. church leaders began an all-out lobbying blitz on the city. Led by Wilson, a group of African American pastors interrupted a D.C. Council meeting in May. The ministers sang “Ain’t Gonna Let Nobody Turn Me Around,” a civil-rights-era chant whose lyrics about “marching up to freedom land” they had adapted to the cause of fees on surfaces impervious to rainfall.

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When the D.C. Council adopted its budget in June, it directed the mayor to grant relief from the river cleanup fee to nonprofit organizations, which are already exempt from property taxes.

But the resulting policy from the administration of Mayor Muriel E. Bowser (D) went far beyond lifting the burden on burial grounds. It offered to dismiss most of the fees owed by any cemetery or religious organization, as long as those fees would amount to at least 0.75 percent of net revenue. Charitable nonprofit groups that aren’t religious were given a tougher standard, with relief provided only if the fees would consume at least 5 percent of net revenue.

Eligible groups would also have to commit to storm-water-management improvements.

The proposal is one that squarely benefits religious organizations.

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Wells, the water board chairman, said in an interview that the city estimates that 800 religious nonprofit groups would qualify for relief, compared to 400 charitable nonprofits and 15 cemeteries. (At least some of those cemeteries are owned by churches.)

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Roth, who is Jewish, said he was particularly offended that a mosque affiliated with the Nation of Islam — whose leader, Louis Farrakhan, has promoted anti-Semitic views — could get more favorable treatment than secular nonprofit groups that combat bigotry.

Denise Krepp, an advisory neighborhood commissioner in Ward 6, said she had been lobbied by the Catholic Church to support the relief proposal. She said she opposed special treatment for any religious organizations — but particularly for the Catholic Church, which she said has not been sufficiently transparent in its handling of sexual abuse allegations against clergy.

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“They’ve got the money, and they can pay. They have no sympathy from me right now,” Krepp said. “You don’t do a carve-out, and right now you certainly don’t do a carve-out for the Catholic Church.”

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Theodore McCarrick, the former archbishop of Washington, was suspended from ministry in June after allegations that he had abused a youth and committed sexual misconduct with adults. McCarrick later resigned from the College of Cardinals. His successor as archbishop, Cardinal Donald Wuerl, stepped down amid accusations that he mishandled abuse complaints while he was bishop in Pittsburgh. In early November, Urbano Vaz­quez, a priest at a Columbia Heights church, was arrested following accusations he sexually abused three teenage girls in 2015.

Ed McFadden, a spokesman for the Archdiocese of Washington, said the archdiocese “would politely disagree” with Krepp’s allegation that it had been secretive in its handling of the clerical abuse issue. Until the Vazquez case, McFadden said, there had not been a claim of abuse made against any priest in the archdiocese in nearly two decades.

“We have been more transparent related to our child-protection policies and the claims of abuse over the last 30 years than many other institutions dealing with this issue,” McFadden said.

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Darcy Hirsh of the Jewish Community Relations Council of Greater Washington said that her organization welcomed the proposed relief package, which she said had been a burden for District synagogues.

However, she said, that “there should not be a double standard” in assessing which nonprofit groups receive discounts and that one way to resolve the issue could be to change how the fees are calculated, using some measure other than how much of a property does not absorb rain.

“We’re looking to find a legislative fix to this,” she said.