Accurate predictive modeling of the ocean’s global carbon and oxygen cycles is challenging because of uncertainties in both biogeochemistry and ocean circulation. Advances over the last decade have made parameter optimization feasible, allowing models to better match observed biogeochemical fields. However, does fitting a biogeochemical model to observed tracers using a circulation with known biases robustly capture the inner workings of the biological pump? Here we embed a mechanistic model of the ocean’s coupled nutrient, carbon, and oxygen cycles into two circulations for the current climate. To assess the effects of biases, one circulation (ACCESS-M) is derived from a climate model and the other from data assimilation of observations (OCIM2). We find that parameter optimization compensates for circulation biases at the expense of altering how the biological pump operates. Tracer observations constrain pump strength and regenerated inventories for both circulations, but ACCESS-M export production optimizes to twice that of OCIM2 to compensate for ACCESS-M having lower sequestration efficiencies driven by less efficient particle transfer and shorter residence times. Idealized simulations forcing complete Southern Ocean nutrient utilization show that the response of the optimized system is sensitive to the embedding circulation. In ACCESS-M, Southern Ocean nutrient and dissolved inorganic carbon (DIC) trapping is partially short circuited by unrealistically deep mixed layers. For both circulations, intense Southern Ocean production deoxygenates Southern-Ocean-sourced deep waters, muting the imprint of circulation biases on oxygen. Our findings highlight that the biological pump’s plumbing needs careful assessment to predict the biogeochemical response to ecological changes, even when optimally matching observations.