The Gulf of Maine (GoME) is a shelf region especially vulnerable to ocean acidification (OA) due to natural conditions of low pH and aragonite saturation states (Ω‐Ar). This study is the first to assess the major oceanic processes controlling seasonal variability of the carbonate system and its linkages with pteropod abundance in Wilkinson Basin in the GoME. Two years of seasonal sampling cruises suggest that water‐column carbonate chemistry in the region undergoes a seasonal cycle, wherein the annual cycle of stratification‐overturn, primary production, respiration‐remineralization and mixing all play important roles, at distinct spatiotemporal scales. Surface production was tightly coupled with remineralization in the benthic nepheloid layer during high production seasons, which results in occasional aragonite undersaturation. From spring to summer, carbonate chemistry in the surface across Wilkinson Basin reflects a transition from a production‐respiration balanced system to a net autotropic system. Mean water‐column Ω‐Ar and abundance of large thecosomatous pteropods show some correlation, although patchiness and discrete cohort reproductive success likely also influence their abundance. Overall, photosynthesis‐respiration is the primary driving force controlling Ω‐Ar variability during the spring‐to‐summer transition as well as over the seasonal cycle. However, calcium carbonate (CaCO3) dissolution appears to occur near bottom in fall and winter when bottom water Ω‐Ar is generally low but slightly above 1. This is accompanied by a decrease in pteropod abundance that is consistent with previous CaCO3 flux trap measurements. The region might experience persistent subsurface aragonite undersaturation in 30–40 years under continued ocean acidification. Key Points Aragonite saturation is primarily driven by photosynthesis and respiration‐remineralization in the water column of the Gulf of Maine Calcium carbonate dissolution appears to occur from fall to winter in the deep portion of the Gulf of Maine Consistent undersaturation of subsurface aragonite saturation is likely to occur in 30–40 years under acidification in the Gulf of Maine