JCMUA violations included releases of untreated sewage into the Hackensack River, Hudson River, Newark Bay and Penhorn Creek.
JCMUA will spend about $52m in repairs and upgrades to its existing infrastructure and pay a civil penalty of $375,000.
Under the settlement, JCMUA is required to comply with its Clean Water Act permit and will conduct evaluations to identify the problems within the system that led to releases of untreated sewage.
JCMUA will also complete repairs to approximately 25,000ft of sewer lines over the next eight years.
JCMUA will spend $550,000 into a supplemental environmental project that will remove privately-owned sewers from homes in several neighborhoods in Jersey City and replace them with direct sewer connections, creating better wastewater collection in those areas.
Combined sewer systems are designed to transport sewage, industrial wastewater and rainwater runoff in the same pipes to wastewater treatment plants.