The billing error has impacted about 18,000 customers, mostly in the city's Point Breeze neighborhood.
Their bills are shooting up, and in some cases, by tens of thousands of dollars.
"The water department thinks I owe them over $13,000," said Chelsea Burns of Point Breeze.
Burns said the news was shocking, considering she lives by herself and her bill is normally about $50.
"If I knew better, I would start bottling it because it's like liquid gold apparently coming out of my faucets," she joked.
More than 200 people on a Point Breeze Facebook group say they received sky-high bills, too.
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"They were saying $20,000, $40,000," said Loretta Tague, who posted her bill on Facebook.
When Tague checked, her bill was also unusually high, a big concern since her payments are automatically debited from her bank account.
"I did log on this morning, first thing and realize that you can put a cap on it," she said. "So, I didn't shut it off but I put a cap on it."
Both Tague and Burns have newly installed water meters, but Susan Crosby, the deputy revenue commissioner said they are not the problem.
She blames a "data" or "file error" from the meter reading company.
"We get the files on a daily basis," said Crosby. "And for some reason, the file that we received on Tuesday was incorrect."
Customers on two routes with new and old meters have been impacted. Crosby said the city learned of the problem on social media Wednesday.
"And what have you done since then?" asked the Troubleshooters.
"Since then, it's been an all-hands-on-deck approach with both our IT team and our communications team," said Crosby.
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The city told the Troubleshooters that the issue will be fixed.
"And we're working to fix it," she said. "We hope to have the fix in place by Friday, early next week at the latest."
The city said it stopped automatic payments that would have debited the incorrect amounts. It is also sending out email alerts and corrected bills to customers.
"What is your message to these customers who are shocked and getting these high bills?" asked the Troubleshooters.
"Just that we understand that in this day and time getting such a high bill can cause a lot of distress," said Crosby. "And we want to let them know that we are working very hard and very quickly to alleviate that so that they don't have to worry about paying these high bills."
"So we have your word that no one will be held responsible for these erroneous amounts?" asked the Troubleshooters.
"All of the amounts that are a result of this billing error that is correct," she said.
Click here if you received one of these high bills.