The production of neurotoxic methylmercury (MeHg) from inorganic Hg and its bioaccumulation in food webs have been reported in marine ecosystems worldwide. However, the concurrent biogeochemical and physical processes affecting ambient levels of MeHg are still poorly characterized. Numerical models offer valuable support to investigating environmental dynamics, by simulating key processes and the non-linear interactions driving the evolution of the state variables in natural system. Shallow coastal environments, encompassing various key and productive ecosystems such as estuaries, lagoons, and bays, are often repositories for anthropogenic pollutants such as Hg, and can act as secondary sources of pollution to the ocean in the long term. We investigated the Hg cycling in a temperate lagoon impacted by past industrial activities (the Venice Lagoon, Mediterranean Sea) by integrating modeling tools with different spatial and temporal scales. Long-term dynamics from the preindustrial to postindustrial phase were simulated with a box model. Time variable Hg loadings were reconstructed based on industrial production rates and emission factors to force the model. Past ecosystem changes, such as eutrophication and alien species invasion, were also taken into account in the model implementation. Annual dynamics for the present state were further investigated at a higher spatial resolution with a model for Hg biogeochemistry and sediment dynamics coupled with a finite element hydrodynamic model. Modeling results, which were validated against available data, highlight the importance of benthic-pelagic exchanges for Hg cycling in the lagoon. However, as inorganic Hg is more affected by sediment particle dynamics, and MeHg by biological processes, the two species show different spatial and temporal distributions.