The Bay Area Air Quality Management District says the settlement covers 19 violations from 2008 and 2009.
Among the violations the company was cited for failing to take flare-gas samples, inadequate measurement of flare gas flows and inaccurate ground level monitoring of hydrogen sulfide.
Air district executive Jack Broadbent says the district has the responsibility to protect the health of residents around refineries. He says any violations, no matter how minor, are not tolerated.
Phillips 66 spokeswoman Janet Grothe said most of the violations were disclosed by the company to the board and were fixed quickly.
The 19th annual Lodi Sandhill Crane Festival this weekend is expected to bring thousands of visitors to see the stately birds.
The Pacific Storm system brought some slight improvement to drought conditions in California and Nevada last week.
The U.S. Environmental Protection Agency is providing more than $30 million to California and Nevada native tribes for water quality and environmental restoration projects.
A program will begin soon in the Eldorado National Forest to remove live or dead vegetation to prevent the spread of wildfires.
The Sacramento Suburban Water District is asking customers to voluntarily cut outdoor watering to one day a week this fall as other water providers move to mandatory restrictions.