Calling stormwater “one of the greatest threats to clean water in Massachusetts,” the Connecticut River Conservancy is joining a lawsuit with other watershed groups against the federal government for its one-year delay in implementing a new stormwater discharge permit for the commonwealth.

The permit would require most Massachusetts cities and towns to reduce stormwater runoff through a combination of public education, investigation of piping and eventually, repairs to prevent runoff.

The suit, filed last September against the federal Environmental Protection Agency and its administrator, Scott Pruitt, is part of a growing national trend in suing the EPA as a way of protecting the environment in reaction to the EPA’s rollback of regulations under the Trump administration.

Local clean water advocates are using this tactic to take a stand against rollbacks that are seen as threatening public health, safety, and quality of life, according to the Connecticut River Conservancy, a nonprofit environmental organization based in Greenfield. The conservancy fears that without action, the one-year delay in implementation of the permit could be extended beyond July.

The Massachusetts so-called “MS4” permit, which is authorized under the federal Clean Water Act, regulates small “municipal separate storm sewer systems” and was issued in 2003 for five years. Since then, it has been administratively continued and has remained in effect during a multiyear, multi-party process for updating the expired permit that began in 2008 and resulted in an update issued by EPA in April 2016.

The new permit was due to take effect last July 1, but according to the Watershed Conservancy, was “abruptly delayed by Pruitt and the EPA just two days before that date.”

The conservancy said this caused existing stormwater projects to move forward with outdated stormwater controls, which will force costly upgrades in the future rather than the lower cost option of adding updated controls at the time of construction.

The delay also ignores the time and money invested by cities and towns that have already implemented new stormwater protection measures in preparation for the new permit to take effect last July, the conservancy said.

At the time the permits were delayed last July, the EPA pointed to the additional costs 260 Massachusetts municipalities would be facing to comply with the new regulations. The city of Lowell was among four litigants that appealed the new regulations.

But at the time, regional EPA spokesman David Deegan told The Lowell Sun in an email, “We spent a lot of time reaching out to communities and listening to their concerns. We published two drafts and paid close attention to the comments we received from the cities and towns. We made many changes in response to those comments … without a big improvement in the way we manage stormwater, we can’t restore water quality in Massachusetts.”

Andrew Fisk, Connecticut River Conservancy executive director, said this week, “We think the EPA’s legal case is fundamentally flawed. Pruitt and the EPA have asked for this delay while permit appeals are being decided, but then in the same breath also asked the court to delay judicial review of the appeals. It is clear that EPA is looking at every maneuver they can find to stop doing the right thing for the public’s water.”

Of particular concern to the nonprofit environmental groups is the public health issue of harmful bacteria flowing to rivers during and after a rainstorm.

Stormwater, also generated by snowmelt, often flows over pavement and rooftops into storm drains, carrying road salt, fecal matter from animals, trash, antifreeze, solvents and other harmful materials into waterways.

About 20 percent of water samples collected by the 54-year-old conservancy and its partners in 2017 from the Connecticut River and its tributaries in Massachusetts showed bacteria levels too high for swimming and boating.

“Delaying the implementation of this updated permit puts our rivers and our water at risk, which also put our citizens and local economies that use and rely on our rivers at risk,” said Fisk. “The EPA is charged with implementing the Clean Water Act for the benefit of the public, yet it did not weigh the public’s interest when it slammed the brakes on the MS4 Permit.”