The settlement requires Shell to make facility upgrades, ensure its hazardous materials are properly managed and develop a plan to sample stormwater.
In a press release, the agency estimates the required improvements will prevent the release of tons of hazardous waste materials into the environment every year.
Shell plans to pay $220,300 to make facility improvements, $142,664 as a civil penalty to the EPA and $38,000 in support of emergency planning and preparedness in Contra Costa County.
The EPA says the company violated several federal Clean Air Act regulations involving the release of sulfuric acid and butane and improper storage of several toxic chemicals.
The agency says the refinery failed to appropriately provide notice after a release of 4,605 pounds of sulfuric acid on Dec. 14, 2013.
The spill took place between 7 a.m. and 8 a.m that day, but Shell told Contra Costa County officials and the California State Warning Center after 11 a.m., according to Randy Sawyer, the county's chief environmental health and hazardous materials officer.
The chemical was released into a storm drain, according to a county report. Shell later said that it was caused by the failure of a storage tank valve.
The violations were uncovered during several EPA inspections between 2014 and 2016.
During one inspection the agency found, in a paint shop, 18 containers of waste stored incorrectly as non-hazardous materials.
Federal inspectors found some hazardous waste containers were left open, others were not labeled and in some cases, waste was treated, stored and disposed without a required permit.
The agency also said Shell did not sample stormwater as it should have from its facility before releasing it.
Bay Area environmental groups blasted the settlement on Tuesday.
"This is like getting fined a nickel for speeding through a school zone," said Hollin Kretzmann, a senior attorney at the Center for Biological Diversity.
"Despite finding that Shell released thousands of pounds of dangerous sulfuric acid and many other violations, EPA's so-called penalty amounts to spare change for one of the world's richest companies," Kretzmann said in an email.
In 2017, Shell made $16 billion in profits, as reported by Reuters.
"It's clear the EPA wants to protect Shell more than the communities threatened by this dirty refinery," Kretzmann said.
Sejal Choksi-Chugh, executive director of San Francisco Baykeeper, says Shell's failure to report spills and comply with hazardous waste laws puts nearby communities and the bay at risk.
"EPA's penalty is insubstantial compared to the real risk posed by the company's misdeeds. Shell officials should be ashamed of their actions, and the company should have been fined an amount that would have ensured they didn't shirk their responsibility to the public again," Choksi-Chugh said.
Shell executives say they will put in place several reforms to make their sampling and reporting of hazardous materials more robust.
"Even though these findings did not result in significant impacts to our community or the environment, we take them seriously and will take the appropriate steps to prevent them from happening again," said Tom Rizzo, Shell refinery general manager, in an emailed statement.
"The Bay Area is home to some of the world's most stringent regulations on industry, and those are standards we don't shy away from," said Shell spokeswoman Ann Notarangelo. "When we fall short of them, we want to immediately report and correct."