A data assimilation technique is used with a simple but widely used marine ecosystem model to optimize poorly known model parameters. A thorough analysis of the a posteriori errors to be expected for the estimated parameters was carried out. The errors have been estimated by calculating the Hessian matrices for different problem formulations based on identical twin experiments. The error analysis revealed inadequacies in the formulation of the optimization problem and insufficiencies of the applied data set. Modifications of the actual problem formulation, which improved the accuracy of the estimated parameters considerably, are discussed. The optimization procedure was applied to real measurements of nitrate and chlorophyll at the Atlantic Bermuda site. The parameter optimization gave poor results. We suggest this to be due to features of the ecosystem that are unresolved by the present model formulation. Our results emphasize the necessity of an error analysis to accompany any parameter optimization study. © 2001 Elsevier Science B.V.