The Keehi Marine Center has agreed to pay nearly $128,000 in penalties after runoff pollution from its boatyard into Keehi Lagoon was found to have violated the federal Clean Water Act, the EPA announced Wednesday.

The boatyard lacked adequate stormwater pollution controls, according to an EPA release. Under the settlement, the center will take steps to reduce the levels of zinc, lead, copper and other contaminants that leak into the lagoon.

“This order will help prevent pollution from reaching Keehi Lagoon and Mamala Bay, protecting fragile coastal ecosystems,” EPA Pacific Southwest Regional Enforcement and Compliance Assurance Division Director Amy Miller said in the release.

In addition to the boatyard, which allows for repairs and maintenance, Keehi Marine Center also operates the 136-slip private marina at the lagoon, according to its website.

The company has already resurfaced its 1.3-acre boatyard to help prevent contaminants at work areas from spilling into the lagoon, according to the EPA. It’s also installed a treatment system and developed pollution prevention plans under a Nov. 3 order.

The settlement to resolve the violations is subject to a 30-day public comment period.