QUINCY — Mayor Thomas Koch said he's "very disappointed" and "outraged" that the federal government, instead of working with Quincy to improve its sewer and storm drain systems, is suing the city for releasing sewage and untreated wastewater into Quincy Bay and Boston Harbor.

On Friday, the same day a tolling agreement to avoid litigation expired, the U.S. attorney's office in Massachusetts filed a lawsuit alleging the city of Quincy violated the Clean Water Act by releasing sewage and untreated wastewater into the Boston Harbor, Dorchester Bay, Quincy Bay and other waterways.

Koch said the city had been in negotiations for more than a year with the the U.S. Environmental Protection Agency, which wanted the city to sign a consent decree that would have forced it to spend tens of millions of dollars to upgrade its sewer and storm drain systems. Koch said the city has already spent tens of millions over the last decade to fix and replace sewer lines to prevent contamination into the storm drains and flood gates.

"The city has not ignored this issue. In fact, quite frankly, we've been proactive on this issue," Koch said in a press conference Friday, where he was joined by U.S. Rep. Stephen Lynch, a South Boston Democrat. "I do not believe the EPA is being reasonable. I think it's a federal government overreach."

Koch said the city is exploring the possibility of countersuing the U.S. Environmental Protection Agency.

The civil complaint filed by the office of U.S. Attorney Andrew E. Lelling alleges that water quality samples collected between 2009 and 2018 showed that Quincy discharged pollutants, including the bacteria E. coli and Enterococcus, onto its beaches and tidal areas along the coastline.

“The Clean Water Act is designed to protect the waters of the United States for the health and enjoyment of its citizens,” Lelling said in a statement. “This complaint demonstrates our commitment to ensuring that our waters and beaches are protected from discharges such as raw sewage and seeks to require that the City of Quincy take the important and necessary steps to do so.”

The complaint also alleges that the water quality samples taken between 2009 and 2013 from Quincy Bay, Sagamore Creek, Town Brook, Town River Bay and Furnace Brook contained ammonia, surfactants and pharmaceutical compounds, which are indicative of sewage waste.

Quincy’s sanitary sewer system overflowed on numerous occasions, according to the complaint, releasing sewage and untreated wastewater.

Koch said one of the issues the government lists in the lawsuit, a leaking sewer line in Squantum, was fixed more than a year and a half ago.

"The reality is we've been at the table meeting on these issues time and time again," Koch said.

The Clean Water Act allows for daily penalties of $37,500 for each violation that occurred on or before Nov. 2, 2015, and $54,833 for each violation occurring after Nov. 2, 2015. The complaint seeks penalties and requests that the court permanently enjoin the city from future violations of the Clean Water Act.

Lynch said he was “very, very surprised” at the federal government’s decision to sue the city, which he said has been “genuine and earnest” in its effort to address the environmental issues. Lynch said the problems often occur during large storms when the storm drain system is overwhelmed

“The systems that were meant to address the weather patterns 20 or 30 years ago are being overwhelmed, but that is not because of the negligence of municipal and state officials. That’s because of climate change,” he said. “We have to recognize that there’s a federal role here to help municipalities build resilience into their systems.”

Bruce Berman, director of strategy and communications at Save the Harbor Save the Bay, said Quincy has been a leader in environmental cleanup, and there have been huge improvements in water quality in the past decade.

“Clean water is a core family value in coastal Massachusetts and the people of Quincy love the sea and their beaches,” he said. “We’re confident that the EPA, DOJ and Quincy will come to an understanding about how best to resolve the remaining water quality problems that affect Wollaston and Quincy’s other beaches.”

Massachusetts Bay, including Wollaston Beach, was one of the most polluted areas in the country in the 1980s because of thousand of gallons of sewage pumped daily into the water from the former treatment plant at the end of Houghs Neck. At one point the beach was so polluted it was closed to both shellfishing and swimming, and the city successfully sued the state for violating of the Clean Water Act.

"We're committed not because the EPA wants us to do something. We're committed because this is the city we love. It's the city we grew up in and the city we're maintaining," Koch said.