An important issue today is to understand in what extent cycling of mercury in the future may be altered in regard to Climate Change. Predictions imply that most of the parameters that determine the global mercury cycle today will change. Laranjo bay (Ria de Aveiro) received, during five decades, a large amount of mercury from a highly contaminated chlor-alkali plant effluent discharge from the industrial Estarreja complex. Due to natural remediation processes, in which layers of less contaminated particles overlap with contaminated sediment, most of the mercury released to the lagoon has been trapped in the deeper layers of sediments. Natural and extreme events, Climate Change, or man-made events (dredging activities of the outlet channel will be conducted in the lagoon) can play an important role in the mercury distribution in Ria de Aveiro, since they may promote the remobilization from the deeper layers of sediment to the water column. Under the extreme events and Climate Change scenarios, detailed information on mercury remobilization and transport in Ria de Aveiro is critical to understand the environmental cycling of mercury and relevant for the development of cost-efficient strategies towards reducing the negative impacts of this metal. This study will provide valuable information on the remobilization and transport of mercury from the historically most contaminated area towards adjacent areas of the lagoon, not only through field monitoring but also through modelling, in a Climate Change scenario (four distinct hydrodynamic scenarios), in order to build a prediction procedure contributing to mitigate future disturbances.