Mollusc aquaculture is a high-value industry that is increasing production rapidly in Europe and across the globe. In recent years, there has been discussion of the potential wide-ranging environmental benefits of this form of food production. One aspect of mollusc aquaculture that has received scrutiny is the production of calcareous shells (CaCO3). Mollusc shell growth has sometimes been described as a sink for atmospheric CO2, as it locks away carbon in solid mineral form. However, more rigorous carbonate chemistry modelling, including concurrent changes in seawater pCO2, pH, dissolved inorganic carbon, and total alkalinity, shows that calcification is a net CO2 source to the atmosphere. Combined with discussions about whether mollusc respiration should be included in carbon footprint modelling, this suggests that greater in-depth understanding is required before shellfish aquaculture can be included in carbon trading schemes and footprint calculations. Here, we show that regional differences in the marine carbonate system can alter the amount of CO2 released per unit CaCO3 formation. Our carbonate chemistry modelling shows that a coastal mussel farm in southern Portugal releases up to ~0.290 g of CO2 per g of CaCO3 shell formed. In comparison, an identical farm in the coastal Baltic Sea would produce up to 33% more CO2 per g of CaCO3 (~0.385 g-CO2·(g-CaCO3)−1). This spatial variability should therefore also be considered if mollusc aquaculture is to be included in future carbon trading schemes, and in planning future expansion of production across the industry.