Runoff containing heavy metals alleged to have come from metal recycling sites in Concord and Manchester have led to a $600,000 legal settlement that will be used to improve water quality in the Merrimack River.

The money is part of a $2 million settlement reached by the Conservation Law Foundation and Schnitzer Steel, a $3.5 billion Oregon firm now known as Radius Recycling. The CLF had filed three lawsuits regarding alleged Clean Water Act violations at 11 scrap metal facilities in Massachusetts and Puerto Rico as well as some in New Hampshire, including sites in Concord off Hall Street at the site of the former Boston & Maine railyard and off Basin Street on the banks of the Merrimack River.

“It was a relatively easy lawsuit to bring: It’s based on their own reporting,” said Heather Govern, vice president of the CLF, said of the suits brought in federal court in three jurisdictions. “Schnitzer has reacted in a responsible way to the allegations. They were willing to settle without continuing litigation and the settlement is quite robust as far as compliance measures and penalties.”

Radius is a huge recycler of metal, a publicly traded company with a reported 3,500 employees throughout North America. Govern said the lawsuit was one of the biggest ever undertaken by the Conservation Law Foundation, and definitely the biggest involving pollution from runoff.

Aside from Concord and Manchester, lawsuits targeted company facilities in Attleboro, Worcester and Everett, Massachusetts, as well as several sites in Puerto Rico.

The main problem in Concord, said Govern and Chelsea Kendall, CLF staff attorney, came from not controlling rainwater runoff that contained heavy metals like lead, zinc, aluminum and copper, as well as suspended solids and some petroleum-related pollutants.

“There are huge piles of uncovered scrap metal and when it rains, the rainwater carries away … really small particles of metal and dissolved metals and other material,” Govern said.

Catch basins and drainage exists at the Concord site “but the current systems are quite rudimentary,” she said. “As we’ve seen from the self-reported data, it’s not doing the job. They’ve committed to putting in more advanced stormwater management systems to separate out the (heavy metals).”

The $600,000 settlement in New Hampshire and Massachusetts will be used by the Merrimack River Watershed Council, which said it would restore eroded shorelines, reducing pollution from stormwater runoff, and potentially also remove outdated dams and replace inadequate culverts that can cause flooding and often hurt fish migration and habitat.

Additionally, The council said it would expand its year-round water sampling on the Merrimack River to better understand the impact of bacteria and other pollutants, and to inform residents of potential risks from pollution.

“The damage done to the river cannot be undone,” said Curt Rogers, Executive Director of the Merrimack River Watershed Council, in a statement. “However, the sizable settlement sends a clear message to current polluters of the potential price to be paid for violating the Clean Waters Act and the funds will have a meaningful impact in moving us towards a cleaner and healthier river.”