The ocean’s “biological pump” significantly modulates atmospheric carbon dioxide levels. However, the complexity and variability of processes involved introduces uncertainty in interpretation of transient observations and future climate projections. Much work has focused on “parametric uncertainty”, particularly determining the exponent(s) of a power-law relationship of sinking particle flux with depth. Varying this relationship’s functional form introduces additional “structural uncertainty”. We use an ocean biogeochemistry model substituting six alternative remineralization profiles fit to a reference power-law curve, to characterize structural uncertainty, which, in atmospheric pCO2 terms, is roughly 50% of the parametric uncertainty associated with varying the power-law exponent within its plausible global range, and similar to uncertainty associated with regional variation in power-law exponents. The substantial contribution of structural uncertainty to total uncertainty highlights the need to improve characterization of biological pump processes, and compare the performance of different profiles within Earth System Models to obtain better constrained climate projections.