JBS USA and the Department of Justice (DOJ) reached a settlement last week over one of the company’s plants’ alleged failure to comply with the Clean Water Act and the Pennsylvania Clean Streams Law, which government officials say caused major fish kills in Pennsylvania waterways.

The agreement requires JBS, which purchased the facility from Smithfield Beef Group in 2008, to improve operations by reconstructing the system that carries water to its waste water treatment plant. The company is also to pay $2 million in fines–$1.9 million in civil penalties and $100,000 in damages.

The facility at the center of the dispute, formerly Moyer Packing Co., located in Franconia Township, PA, was charged with dumping pollutants into Skippack Creek, a tributary of the Perkiomen Creek and the Schuylkill River, over a five year period. According to the U.S. Attorney’s Office, the pollution caused fish kills in the Skippack Creek on: August 10, 2007 (16,461 fish), December 5, 2007 (1,754 fish), and June 10, 2008 (6,500 fish).

The case was jointly investigated by the Environmental Protection Agency, the Pennsylvania Department of Environmental Protection, and the Pennsylvania Fish and Boat Commission. The DOJ filed complaint against JBS in 2008.

“Our waterways should not become a casualty of business decisions,” said U.S. Attorney Zane David Memeger, in a statement. “Provisions such as the federal Clean Water Act and the Pennsylvania Clean Streams Law exist to ensure that our waterways do not become sewers, that the health of our ecosystem is not compromised, and that the health of our citizens is not put at risk.”

The Environmental Protection Agency’s Mid-Atlantic Regional Administrator, Shawn M. Garvin, said the agreement represents “a major step forward in protecting the waters of the Schuylkill River basin which supplies drinking water to more than 1.7 million people, and provides a vital source of aquatic life and recreation for the region.”

JBS is currently upgrading its facility with a $6 million wastewater treatment plant. According DOJ, the plant’s operations, which include a rendering facility, produce approximately 180 million pounds of boxed beef and 117 million pounds of ground beef annually.

“I will say that the new owners have been far more responsive even though the majority of the violations took place prior to their purchase of the plant in 2008,” Pennsylvania Department of Environmental Protection spokeswoman Deborah Fries told Meatingplace, an online industry news hub. “They’ve done the things we’ve asked them to do.”

The plant in Franconia employs 1,600 people and slaughters some 2,000 head of cattle per day, according to Meatingplace.