Specifically, it said the plant was "engaging in unlawful dumping of waste and chemicals."
Instead of using required chemicals in antipollution scrubbers, it said, the plant simply ran water through the devices. And when there was air-quality testing, it provided inaccurate information, the suit said.
Synagro spokeswoman Jamie Kinder rejected those allegations.
"Our Philadelphia plant is a state-of-the-art facility that provides tremendous benefits to the city and has always operated in full compliance with all applicable regulations," she said in a statement. "We deny the accusations made by the plaintiffs and will vigorously defend ourselves to the full extent of the law."
Attorneys for the former supervisors, Anthony Chaney and Christopher Kennedy, declined to discuss the case.
According to the suit, Chaney and Kennedy, both from Delaware, were fired "for refusing to engage in criminal acts" at the company's direction. In addition to Synagro, the firm's local affiliate, Philadelphia Biosolids L.L.C., is listed as a defendant.
The suit said Kennedy and Chaney complained to Synagro's local managers about the problems in July. A month later, it said, they were laid off.
It said that no one else was laid off and that the two eventually were fired.
The suit said Synagro violated the Pennsylvania Whistleblower Act, which prohibits retaliation because employees report "incidents of wrongdoing."
The Philadelphia plant, which replaced a city-run facility, for years was a source of political controversy.
City Council's 2008 approval of Synagro's contract was an especially heated event.
In an unrelated earlier suit against Synagro, a federal judge wrote that the company's actions in obtaining the approval were "a primer on how to procure multimillion-dollar service contracts with the city."
In a recent opinion, U.S. District Judge Stewart Dalzell described how money flowed from Synagro consultant Hiriam Hicks to a community activist who rounded up homeless people to cheer on Council as it approved the firm's contract.
"The entire day was a scene of chaos," wrote Dalzell, who is overseeing Hicks' suit against the waste company. Hicks was to receive $9 million for his work, including helping win Council approval.
Before Mayor Nutter approved Synagro's 23-year contract, he cut the total contact price by the $9 million.
Nutter spokesman Mark McDonald did not respond to requests for comment.
Synagro is the nation's largest processor of sludge and waste, operating in about 600 municipalities in 36 states.
Before Synagro won its Philadelphia contract, it was tainted by a 2007 bribery scandal that sent former Detroit city officials to prison.
The scandal involved the firm's effort to win a $1.2 billion contract. Among those who went to prison was former City Councilwoman Monica Conyers, wife of U.S. Rep. John Conyers.
Contact Mark Fazlollah at 215-854-5831 or firstname.lastname@example.org