The Martinez Refining Company has agreed to pay $4.482 million to settle allegations of federal Clean Water Act violations at its refinery, the San Francisco Bay Regional Water Quality Control Board said Thursday. The refinery allegedly discharged millions of gallons of wastewater from oil refinery processes, which harmed water quality and threatened aquatic life in marshes linked to the Carquinez Strait. … The water board found three cases of unauthorized discharges into nearby marshes.