Results of the first survey of acidification in Bellingham Bay demonstrate corrosive water in the center of the bay. Low levels of pH (7.5) and aragonite saturation state (0.5) were observed near the region of seasonal hypoxia. Measurements of the input of dissolved inorganic carbon and alkalinity from the Nooksack River, sediment flux, the Post Point WWTP, and deep water, along with measurements of respiration indicate that relatively high rates of respiration in the bay are largely responsible for the acidic water. Sediments are an important contribution to alkalinity. Model results suggest that acidification is seasonal and that water column pH is affected by both respiration and rates of mean circulation in the bay.