San Francisco Baykeeper filed a federal suit to address violations of the federal Clean Water Act by the city of Berkeley and Community Conservation Centers, Inc. on Wednesday, alleging that the defendants are discharging polluted stormwater into the bay.

According to the complaint, the polluted water originates from the Berkeley Transfer Station and the Community Conservation Centers’ recycling center.

The benefit of filing a federal case is that it will be overseen by a judge who can function as an overseer should issues arise during the negotiations, according to managing attorney at Baykeeper George Torgun.

“A lawsuit is required in order to invoke the jurisdiction of the court,” said Zach Cowan, an attorney for the city of Berkeley.

Baykeeper, a nonprofit organization that aims to protect the water quality of the San Francisco Bay, targets industrial sites after reviewing data regarding pollutants released in the area.

The transfer station and recycling center process trash, compost and recycling for transfer to landfills. These facilities — which conduct some operations outdoors — process pollutants such as iron, aluminum and zinc, which can then contaminate already-polluted stormwater.

“Stormwater is essentially rainfall that goes into the ocean, (but) the real problem is biological,” said campus professor John Dracup. “It can hold viruses, bacteria and pathogens of various kinds.”

Stormwater runoff has been recognized as a leading polluter of the water quality of the San Francisco Bay, according to the complaint. Polluted rainwater flowing from local industrial facilities can cause harm to humans and aquatic life.

According to Torgun, industrial facilities have a general state permit that limits the amount of stormwater pollutants that facilities can release, in accordance with the Industrial General Permit for stormwater. Torgun alleged that in the last five years, the city and Community Conservation Centers, Inc. have exceeded this limit, which is considered a violation of the Clean Water Act.

Upon reviewing pollution data for the city of Berkeley in 2015, Baykeeper discovered discharges of polluted stormwater. Allegations of violation in the complaint date back to 2010 — which is within the Clean Water Act five-year statute of limitation, according to Torgun.

To address the violations, negotiations between the parties started after Baykeeper sent the city of Berkeley a 60-day notice of intent to file the lawsuit Nov. 6.

“The filing of the lawsuit was expected and is a normal step in the resolution of this type of case,” said city spokesperson Matthai Chakko, adding that the parties have been “actively working” to reach an agreement.

Torgun said the city has been cooperative during negotiations and is planning to make improvements on the sites.

“The city knows that improvements need to be made such as new filters and better underground tanks, (and) we are looking at a two- to three-year agreement to give the city time to reinforce improvements,” Torgun said. “The case will be over soon.”

Contact Sooyoung Hu at [email protected] and follow her on Twitter at @SHu_DCal.