A U.S. District Court judge dealt a blow Tuesday to a local nonprofit’s case against Baltimore City over failures at its wastewater treatment plants, denying a motion that would have required certain improvements at the facilities.

The environmental nonprofit, Blue Water Baltimore, sued the city late last year under the federal Clean Water Act, arguing that the court should force Baltimore’s two wastewater treatment plants to come into compliance with the law and possibly levy a financial penalty.

This summer, Blue Water filed a motion asking the court for an injunction that would require specific improvements within both the Back River and Patapsco Wastewater Treatment plants. The injunction also would have required public notification when the plant releases more bacteria into local waterways than permitted, in addition to signage explaining bacteria issues at key areas along the Baltimore-area waterfront.

Federal Judge Lydia Kay Griggsby denied Blue Water’s motion Tuesday without prejudice, meaning it could be brought forward again. But she will require the city to submit updates to the court about the plants every 30 days.

The overall case about the plants’ Clean Water Act violations will continue to be litigated.

In her decision Tuesday, Griggsby wrote that Blue Water is “likely to succeed on the merits of at least some of its Clean Water Act claims,” writing that the city’s own data reports have shown more than 250 permit violations at the two plants.

But the nonprofit failed to show that there would be “irreparable harm” if the court didn’t intervene in the repair effort at the two plants, Griggsby wrote.

Plus, many of Blue Water’s requests mirrored the steps the city already agreed to undertake at the plants, at the request of the state, according to her order.

“The Court is concerned that issuing the requested injunction would force the City to comply with parallel actions to remedy the violations at Back River and Patapsco,” Griggsby wrote. “Such a result could have the unintended consequence of further delaying the much-needed improvements that BWB identifies in its motion.”

Angela Haren, a senior attorney for the Chesapeake Legal Alliance, which is representing Blue Water, said that the court’s decision was at least a partial victory for the nonprofit, since the court required monthly updates from the city and left open the possibility of filing for an injunction again if conditions at the plants worsen.

”I think we’re in a good position,” Haren said, “because the federal court understands the severity of the issues at play here and they made it very clear that they want to see expeditious progress.”

An attorney representing Baltimore City declined to comment further on the ruling, as did Baltimore City’s Department of Public Works, which runs the two plants.

In its responses to Blue Water’s motion, Baltimore maintained that court action isn’t warranted or necessary, particularly because the Maryland Environmental Service was dispatched to help make improvements at the Back River Wastewater Treatment Plant, and the water released by the Dundalk plant currently meets standards, though recent state inspections show internal equipment problems have persisted.

No such arrangement is in place at the Patapsco Wastewater Treatment Plant in Curtis Bay, where state environmental inspectors have documented continuing problems with the water flowing from the facility into the Patapsco River.

During an initial July hearing on Blue Water’s motion, Griggsby said the nonprofit hadn’t done enough to prove there would be “irreparable harm” without the court’s intervention. She gave the group a second chance, though, and allowed it to submit a filing focused solely on that topic.

Ultimately, she still denied the motion.

The state also has a case against the city over the plants, which officials have said could yield a consent decree with enforceable requirements for the facilities.

One way or another, Blue Water Baltimore is still looking for deadlines for improvements at the plants, Haren said.

“Our overarching goal has never changed from the beginning,” she said. “And that is to bring these plants into compliance as quickly as possible and to have an enforceable agreement with specific deadlines.”