The San Francisco Bay Regional Water Quality Control Board said ConocoPhillips released between 2.5 million to 7.6 million gallons of toxic chemicals from its Rodeo refinery during a five-month stretch in 2008.
The waste from the Rodeo refinery included copper, selenium, chlorine and other byproducts from refining processes, the San Francisco Chronicle reports.
Water-quality regulators said the wastewater treatment facility at the Rodeo refinery was overwhelmed by storm runoff from January to May 2008.
"The system is designed to handle a certain flow over a certain period of time -- there are certain things the operator can do when there's bad weather coming," said David Clegern, spokesman for California's water control board in Sacramento. "Our issue was that they didn't seem to respond well."
The company has the right to contest the fine at a March 10 hearing or channel the $490,000 to an environmental project that would offset the damage from the San Pablo spill.
ConocoPhillips said it was reviewing the penalty.