A bioaccumulation model to predict concentrations of s-triazine herbicides in the macroalgae Ulva rigida and in clams Tapes philippinarum has been implemented, calibrated and validated. The model uses input data from a 3D biogeochemical model that provides biomasses in the different compartments, i.e. phytoplankton, zooplankton and bacteria; and from a 3D fate model that provides the herbicides concentrations in the water column as well as in the sediments. Simulated data were compared with experimental data collected during a set of sampling campaigns carried out in 2004 and 2005 in the Sacca di Goro lagoon (Northern Adriatic). The model predicts correctly the concentrations of herbicides measured in Ulva rigida and reproduces with good agreement the values of concentration of herbicides found in clams. Furthermore, the simulated spatial and temporal dynamics in the biota compartment, following those of the water and sediments, are also in agreement with the experimental data. This integrated approach combining biogeochemical, fate and bioaccumulation models provide an overall assessment of the importance of the different environmental compartments and it can also support the testing of different management strategies to improve ecosystem state and functioning. Further research is necessary to elucidate the role and importance of the metabolism of these compounds by clams.