In this study it was evaluated whether the ECOPATH with ECOSIM software could be used as a platform to facilitate the construction of models and study of transport and accumulation of radionuclides in aquatic food webs. The evaluation was based upon a food web model of carbon (C) and carbon-14 ((14)C) flow for a coastal area in the Baltic Sea, the ECOPATH, the ECOSIM and the ECOTRACE models. The original carbon flows and assumptions were easily incorporated into the ECOPATH and ECOSIM modelling environment. The new model was also well suited to drive a (14)C flow model (ECOTRACE) for each of the organisms included. ECOTRACE estimated steady-state concentrations of (14)C that were between 73 and 142% of the original flows. The results clearly show that there is great potential for a successful development of this approach for integrating scientific knowledge about food webs and radioecological models for aquatic systems.