Abstract. The impact of deglaciation in Glacier Bay has been observed to seasonally influence the biogeochemistry of this marine system. The influence from surrounding glaciers, particularly tidewater glaciers, has the potential to affect the efficiency and structure of the marine food web within Glacier Bay. To assess the magnitude and the spatial and temporal variability in net community production in a glaciated fjord, we measured dissolved inorganic carbon, inorganic macronutrients, dissolved oxygen, and particulate organic carbon between July 2011 and July 2012 in Glacier Bay, Alaska. High net community production rates were observed across the bay (~ 54 to ~ 81 mmol C m⁻² d⁻¹) between the summer and fall of 2011. However, between the fall and winter, as well as between the winter and spring of 2012, air–sea fluxes of carbon dioxide and organic matter respiration made net community production rates negative across most of the bay as inorganic carbon and macronutrient concentrations returned to pre-bloom levels. The highest organic carbon production occurred within the west arm between the summer and fall of 2011 with ~ 4.5 × 10⁵ kg C d⁻¹. Bay-wide, there was carbon production of ~ 9.2 × 10⁵ g C d⁻¹ between the summer and fall. Respiration and air–sea gas exchange were the dominant drivers of carbon chemistry between the fall and winter of 2012. The substantial spatial and temporal variability in our net community production estimates may reflect glacial influences within the bay, as meltwater is depleted in macronutrients relative to marine waters entering from the Gulf of Alaska in the middle and lower parts of the bay. Further glacial retreat will likely lead to additional modifications in the carbon biogeochemistry of Glacier Bay, with unknown consequences for the local marine food web, which includes many species of marine mammals.