CHICAGO (CBS) — When it comes to water meters in Chicago, churches are getting by on a wing and a prayer.

As WBBM Newsradio’s Felicia Middlebrooks reports, for many years, churches and other non-profits – more than 6,000 of them – have been granted free water service from the city of Chicago.

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LISTEN: WBBM Newsradio’s Felicia Middlebrooks reports

Now, the Chicago Sun-Times reports, they’re being slowly weaned from dependency with deep discounts in their water bills.

But having to pay a new bill bills isn’t the only challenge. The Sun-Times reports the churches are also having to install water meters – a costly and burdensome proposition for struggling churches.

For one example, St. Paul’s Church-by-the-Lake, at 7100 N. Ashland Blvd., will have to pay $11,000 to install an underground water meter in its 98-year-old building, the Sun-Times reported.

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Churches and other nonprofits have also calculated the bills they will have to pay – an exercise that has resulted in sticker shock.

Back in December, the Chicago Archdiocese said it expected a bill of around $2 million from the city.

Projected numbers were also staggering for some larger Catholic institutions. Misericordia, home to 600 developmentally disabled kids and adults, faces a $500,000 annual water bill. For Holy Name Cathedral, it will be $100,000 a year, CBS 2’s Derrick Blakley reported in December.

City Water Management department officials say 400 churches still have no water meters, despite being told to install them so months ago, the newspaper reports.

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The decision to end free water service for nonprofits came as part of Mayor Rahm Emanuel’s 2012 budget. The bills will be phased in with increases over the course of four years.