Maryland environmental regulators have fined a South Baltimore scrapyard $50,000 for allowing toxic metals and oil to wash into the Patapsco River.

The agreement comes nearly two years after officials first found that the company was violating its permits.

As part of a settlement with the Maryland Department of the Environment, the Baltimore Scrap Corp. also agreed to spend at least $750,000 on systems to filter stormwater runoff that washes over its property and into the harbor near Fort McHenry.

The company, which collects and recycles metals at a yard in the Fairfield area, also is being required to test the contents of its runoff more frequently.

State Environment Secretary Ben Grumbles said the settlement announced last week ends a “long” negotiation with the company and sends “a strong signal to all that industrial stormwater violations will not be tolerated.”

Department inspectors first observed problems on the site in March 2016.

Environmental groups that were also party to the settlement said the agreement addresses long-standing hazards to human health and Chesapeake Bay ecosystems. Blue Water Baltimore, a local advocacy group, and the Washington-based Environmental Integrity Project had threatened Baltimore Scrap with a lawsuit under the federal Clean Water Act.

“Our agreement lays a clear path for improvements to the site’s stormwater management so that its stormwater is properly treated and does not contaminate the harbor,” said Angela Haren, the Baltimore Harbor Waterkeeper and director of advocacy for Blue Water.

David Simon, president of Baltimore Scrap, said the company’s low-lying property can be inundated with stormwater from across the largely paved, industrial neighborhood.

The company has spent $800,000 on stormwater-related projects since December 2014, including a street sweeper, he said, and expects to spend $750,000 to $900,000 more to reduce the volume of stormwater across its yard.

“Improvements made by us over the last two years have significantly limited that flow,” Simon said.

Recent sample testing has shown levels of copper in the yard’s runoff fall “well below” levels established in its runoff permits, he said.

The settlement also imposes penalties if the scrap company does not keep its promises, including $500 fines for oil or gas contamination and up to $2,750 fines any time it exceeds limits on discharges of aluminum, iron, lead zinc and copper.

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