Calcium carbonate (CaCO3) mineral saturation states for aragonite (Ωaragonite) and calcite (Ωcalcite) are calculated for waters of the Chukchi Sea shelf and Canada Basin of the western Arctic Ocean during the Shelf-Basin Interactions project from 2002 to 2004. On the Chukchi Sea shelf, a strong seasonality and vertical differentiation of aragonite and calcite saturation states was observed. During the summertime sea ice retreat period, high rates of phytoplankton primary production and net community production act to increase the Ωaragonite and Ωcalcite of surface waters, while subsurface waters become undersaturated with respect to aragonite due primarily to remineralization of organic matter to CO2. This seasonal “phytoplankton-carbonate saturation state” interaction induces strong undersaturation of aragonite (Ωaragonite = <0.7–1) at ∼40–150 m depth in the northern Chukchi Sea and in the Canada Basin within upper halocline waters at ∼100–200 m depth. Patches of aragonite undersaturated surface water were also found in the Canada Basin resulting from significant sea ice melt contributions (>10%). The seasonal aragonite undersaturation of waters observed on the Chukchi Sea shelf is likely a recent phenomenon that results from the uptake of anthropogenic CO2 and subsequent ocean acidification, with seasonality of saturation states superimposed by biological processes. These undersaturated waters are potentially highly corrosive to calcifying benthic fauna (e.g., bivalves and echinoderms) found on the shelf, with implications for the food sources of large benthic feeding mammals (e.g., walrus, gray whales, and bearded seals). The benthic ecosystem of the Chukchi Sea (and other Arctic Ocean shelves) is thus potentially vulnerable to future ocean acidification and suppression of CaCO3 saturation states.