The present paper describes the application of a state-of-the-art model to two lakes in central Italy (Trasimeno and Monterosi) for the assessment of migration parameters of (137)Cs and (90)Sr (migration velocity to sediment, transfer rates from sediment to water and to bottom sediment). Applications of a compartment model and a model based on the diffusion equation to predict the behaviour of pollutants in water and through bottom sediment are presented and discussed. The application of the diffusion equation shows some difficulties of a general nature and typical of such a modelling approach. Moreover, there is no evidence of significant improvements of the model performances when the diffusion equation is applied. Very low levels of sedimentation rate of suspended matter in Lake Monterosi were evaluated by the quantitative assessment of radiocaesium migrating to bottom sediment. This suggests that, in this lake, the removal of radionuclide from the water column is mainly due to the turbulent mixing of bottom sediment causing radionuclide burial.