Maya von Rossum, the network's leader, said Soil Safe had not been responsive in the months following the notice.
"The silence that we've experienced, there really does not seem to be any effort from them to move forward," she said.
Soil Safe, a Maryland-based company, could not be reached for comment Tuesday.
In October, president and chief executive Mark Smith denied the claims now presented in the suit.
"Our operation is carefully regulated by DEP," Smith said at the time.
The riverkeeper network alleges that the facility has not been meeting certain state permit requirements and regulations, arguing that the company's own reports to the Department of Environmental Protection showed detections of benzo(a)pyrene above residential standards. The contaminant contains carcinogens.
The Soil Safe facility neighbors wetlands adjacent to Birch Creek, which connects to the Delaware River. The practices have "resulted in the placement of contaminants . . . which will leach into groundwater and/or surface waters," the suit states.
DEP spokesman Larry Hajna said the department would not comment on pending litigation, but said several compliance issues at the facility had been corrected.
Hajna added that the department found during an October inspection that piles of soil set for processing were larger than permissible, and he said the department would address the issue with the company.
County spokeswoman Debra Sellitto said: "If that soil wasn't meeting standards, I'm sure we would be notified by the state agencies."
The network asks the court to force Soil Safe to cease its Logan operations until it addresses the alleged offenses.
The company is on track to build a soil-recycling facility in Carteret, Middlesex County, that has also been criticized by environmentalists.