Numerical Earth System Models are generic tools used to extrapolate present climate conditions into a warming future and to explore geoengineering options. Most of the current‐generation models feature a simple pelagic biogeochemical model component that is embedded into a three‐dimensional ocean general circulation model. The dynamics of these biogeochemical model components is essentially controlled by so‐called model parameters most of which are poorly known. Here we explore the feasibility to estimate these parameters in a full‐fledged three‐dimensional Earth System Model by minimizing the misfit to noisy observations. The focus is on parameter identifiability. Based on earlier studies, we illustrate problems in determining a unique estimate of those parameters that prescribe the limiting effect of nutrient‐ and light‐depleted conditions on carbon assimilation by autotrophic phytoplankton. Our results showcase that for typical models and evaluation metrics no meaningful “best” unique parameter set exists. We find very different parameter sets which are, on the one hand, equally consistent with our (synthetic) historical observations while, on the other hand, they propose strikingly differing projections into a warming climate.