US ATTORNEY ANDREW LELLING sued the city of Quincy on Friday, alleging the municipality is violating the Clean Water Act by dumping untreated sewage into Boston Harbor, Dorchester Bay, and Quincy Bay.

In a statement, Lelling said his proof can be found in water samples collected from 2009 through 2018.The samples show the city dumped pollutants that carried bacteria such as E.Coli and Enterococcus onto Quincy beaches and tidal areas along the coastline.

Additional samples from Quincy Bay, Sagamore Creek, Town Brook, Town River Bay, and Furnace Brook from the period 2009 through 2013 showed the discharge of ammonia, surfactants, and pharmaceutical compounds, which the Environmental Protection Agency defines as sewage waste.

The federal complaint also says that the area sewer system overflowed many times in Quincy, discharging untreated wastewater and sewage.

Quincy Mayor Thomas Koch didn’t dispute the claims made by the US Attorney’s office, but called the lawsuit “overreaching” and “too aggressive.” He even threatened to pursue a countersuit, although the basis for such a lawsuit was not clear.

Koch insisted the area’s waterways are “safe for swimming,” and that the municipality has actually been “proactive” in working with the Environmental Protection Agency over many years to deal with environmental challenges related to sewage.

“We’re poised to spend $10 million this year on both sewer and stormwater, which is something we’ve been planning,” Koch said at a press conference in his office.

Quincy’s city solicitor, Jim Timmins, said the municipality’s attorneys and officials from the EPA had been meeting every few months up until the fall of 2018. Timmins said the city had been hit with fines by the EPA, but he said he couldn’t estimate how much the city owes. He said the city had suggested using the fine money to fix the environmental problems, but the EPA rejected that approach.

An agreement between the city and the EPA put the statute of limitations on the violations on pause while the two sides tried to work things out. It expired on Friday.

US Rep. Stephen Lynch joined Koch at his press conference and said he wished the EPA had shown “a little patience.” Lynch said the city’s efforts to address its environmental problems “have been genuine” and called the suit “a step backward.”

The lawsuit comes more than 20 years after the region began spending billions of dollars to clean up Boston Harbor, which once was the disposal site for the daily waste of Boston and surrounding communities. The harbor cleanup started with a lawsuit against a state agency initiated by former Quincy city solicitor William Golden, who during a run along Wollaston Beach took umbrage at bits of raw sewage in the sand.

According to the Clean Water Act, it is illegal to discharge pollutants into navigable waters without a permit. “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 US Attorney’s office said in a statement.

The Clean Water Act allows for daily penalties of $37,500 for each violation occurring on or before Nov. 2, 2015, and $54,833 for each violation that happened after that date. In its lawsuit, the federal government is seeking financial penalties and a prohibition against future violations of the Clean Water Act.

“This complaint represents a critical step in the ongoing cleanup of Boston Harbor and nearby urban rivers,” said Deb Szaro, acting regional administrator of EPA’s New England region.