It is not well understood whether coastal upwelling is a net CO₂ source to the atmosphere or a net CO₂ sink to the ocean due to high temporal variability of air–sea CO₂ exchange (CO₂ flux) in coastal upwelling zones. Upwelling transports heterotrophic, CO₂ enriched water to the surface and releases CO₂ to the atmosphere, whereas the presence of nutrient-rich water at the surface supports high primary production and atmospheric CO₂ uptake. To quantify the effects of upwelling on CO₂ flux, we measured CO₂ flux at a coastal upwelling site off of Bodega Bay, California, with the eddy covariance technique during the summer of 2007 and the fall of 2008, and the bulk method with partial pressure of CO₂ of surface water (pCO₂) data from November 2010 to July 2011. Variations in sea surface temperatures (SST) and alongshore wind velocity suggest that the measurement period in 2007 coincided with a typical early summer upwelling period and the measurement period in 2008 was during a typical fall relaxation period. A strong source of CO₂ (~ 1.5 ± 7 SD (standard deviation) g C m⁻² day⁻¹) from the ocean to the atmosphere during the upwelling period was concurrent with high salinity, low SST, and low chlorophyll density. In contrast, a weak source of CO₂ flux (~ 0.2 ± 3 SD g C m⁻² day⁻¹) was observed with low salinity, high SST and high chlorophyll density during the relaxation period. Similarly, the sink and source balance of CO₂ flux was highly related to salinity and SST during the pCO₂ measurement periods; high salinity and low SST corresponded to high pCO₂, and vice versa. We estimated that the coastal area off Bodega Bay was likely an overall source of CO₂ to the atmosphere based on the following conclusions: (1) the overall CO₂ flux estimated from both eddy covariance and pCO₂ measurements showed a source of CO₂; (2) although the relaxation period during the 2008 measurements were favorable to CO₂ uptake, CO₂ flux during this period was still a slight source; (3) salinity and SST were found to be good predictors of the CO₂ flux for both eddy covariance and pCO₂ measurements, and 99% of the historical SST and salinity data available between 1988 and 2011 fell within the range of our observations in May–June 2007, August–September 2008 and November 2010–July~2011, which indicates that our data set was representative of the annual variations in the sea state. Based on the developed relationship between pCO₂, SST and salinity, the study area between 1988 and 2011 was estimated to be an annual source of CO₂ of ~ 35 mol C m⁻² yr⁻¹. The peak monthly CO₂ flux of ~ 7 mol C m⁻² month⁻¹ accounted for almost 30% of the dissolved inorganic carbon in the surface mixed layer.