Water column pH and carbonate mineral saturation states were calculated from dissolved inorganic carbon (DIC) and total alkalinity data collected over the eastern Bering Sea shelf in the spring and summer of 2008. The saturation states (Ω) of the two most important carbonate minerals, calcite (Ωcalcite) and aragonite (Ωaragonite) were strongly coupled to terrestrial runoff from the Yukon and Kuskokwim rivers, primary production in the surface waters, and remineralization of organic matter at depth over the shelf. In spring, before ice melt occurred, pH over the shelf was largely confined to a range of 7.9–8.1 and Ωcalcite and Ωaragonite ranged from 1.5 to 3.0 and 0.8 to 2.0, respectively. At the stations closest to river outflows, aragonite was undersaturated in the water column from the surface to the bottom. During the summer sea ice retreat, high rates of primary production consumed DIC in the mixed layer, which increased pH and Ωcalcite and Ωaragonite. However, Ωcalcite and Ωaragonite decreased by ∼0.3 in the bottom waters over the middle and outer shelf. Over the northern shelf, where export production is highest, Ωaragonite decreased by ∼0.35 and became highly undersaturated. The observed suppression and undersaturation of Ωcalcite and Ωaragonite in the eastern Bering Sea are correlated with anthropogenic carbon dioxide uptake into the ocean and will likely be exacerbated under business-as-usual emission scenarios. Therefore, ocean acidification could threaten some benthic and pelagic calcifying organisms across the Bering Sea shelf in the coming decades.