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.
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.
The increase in the number of wildfires in California and the western U.S. may partly be caused by climate change.
The San Joaquin Valley enjoyed three weeks of healthy air in July for the first time in 20 years.
The California Fish and Game Commission voted Wednesday to ban bobcat trapping in the state.