Church leaders took a “leap of faith” Wednesday and got behind Mayor Rahm Emanuel’s compromise plan to charge non-profits for city water, after some last-second lobbying that ended with unanimous City Council approval.

The city will now charge non-profits based on a sliding scale, determined by their net assets. Groups and churches with less than $1 million in net assets will still get free water, while groups that are worth more than $250 million would pay full price.

Emanuel, aldermen and religious leaders whispered near the City Council bathrooms moments before the roll call vote - a rare scene for a legislative process where most votes are decided long before they hit the council floor.

A coalition of religious groups had objected to the plan, arguing that some old churches wouldn’t get a break because they’re situated on valuable land. Chicago’s Catholic leaders were also worried that their 200 churches and 90 schools wouldn’t qualify for any individual exemptions because they are all technically owned by one entity, the Archdiocese of Chicago.

Coalition leaders claim they had the City Council votes to block the mayor’s plan, but withdrew their opposition after gaining assurances that administrative rules would later be written in their favor.

“In exchange for that commitment, we have - we have said we will support the passage of the ordinance today, and we will work it out,” said Chancellor Jim Lago, with the Archdiocese of Chicago. “It’s a leap of faith, and we’re looking for the goodwill of those who will be in the room with us, and we expect that.”

Lago would not say whether he trusted Emanuel to make sure nonprofits don’t take a big hit when the rules for collecting water fees are written, but he said negotiations would continue in the coming weeks.

The mayor took heat from Chicago’s non-profit community when he first proposed taking away free water as part of his plan to balance the city budget in 2011. He backed off a bit with his compromise proposal last month, but church leaders were concerned about how the city would calculate net assets.

After Wednesday’s City Council vote, Emanuel maintained he struck a fair balance.

“I think we’ve done it in a thoughtful way, reflective of every one of the non-for profits’ and religious entities’ different roles in the community - meaning, their net value - but nonetheless ended the practice where the taxpayers were on the hook for everybody else,” Emanuel said.

During his campaign, Emanuel vowed to stop giving away city water and sewer service to nonprofits - a freebie he estimates costs the city $20 million a year.

Alex Keefe is a WBEZ political reporter. Follow him @akeefe.