The lawsuit accused refinery operators of a chain of failures that allowed the oil, which totaled about 420 gallons, to enter the water at the Shell Wharf in Martinez on Jan. 2, 2006.
The problem started when a contractor reportedly failed to adequately tighten bolts after repairing a pipe at the wharf, according to the district attorney's office.
The oil that leaked out of the pipe should have been contained in the wharf's containment system, and alarms and pumps on that system should have been activated, but apparently were not, according to the district attorney's office.
Refinery employees didn't discover the leak until the oil, which was a feed oil similar to a marine fuel oil, was already in the water.
The leak was discovered at about 4:30 a.m., right after a heavy rainstorm, when refinery employees reported seeing patches of oil on the water near the wharf, refinery spokesman Steve Lesher said.
Refinery employees acted immediately to stop the leak and contain the spill, but some of the oil had already escaped and later made its way into the Martinez Marina, where about 75 boats were found with oil rings around their hulls.
Lesher said the company has settled all claims with individual boat owners and paid to have all the boats cleaned.
The California Department of Fish and Game's Office of Spill Prevention and Response also responded to the spill and investigated the series of events that led up to it, according to the district attorney's office.
At the time, Fish and Game biologists reported finding no impact on plants or wildlife in the area.
Shell employees did, however, clean many rocks by hand, Lesher said.
Refinery officials also worked with the U.S. Coast Guard and the county health department, and paid for the Marine Spill Response Corporation to help with the cleanup.
In its settlement, Equilon Enterprises LLC, which operates the Shell Martinez Refinery, agreed to pay a civil penalty of $250,000 to Fish and Game and $50,000 to the city of Martinez, which will use the finds for a community project along the waterfront, according to Lesher.
The company paid an additional $10,000 to cover the Department of Fish and Game's response costs.
The refinery has also made several improvements to the wharf containment system, including new pumps, alarms and instrumentation and enhanced training and procedures for personnel, according to Lesher.