The Gulf of Trieste (Northern Adriatic) is subject to mercury pollution from a former mercury mine in Idrija, located along a river which transports mercury-contaminated sediments into the Gulf. Concentrations in suspended and bottom sediments are up to two orders of magnitude higher than in the central and southern Adriatic. Extensive research has been carried out on measurements and modelling of the transport and fate of mercury in the Gulf. Two- and three-dimensional models have been developed to include the influence of the significant advective transport due to currents. Wind, thermohaline forcing, and the Soca river momentum are the most important forcing factors. A two-dimensional model simulated the transport of non-methylated and methylated mercury in dissolved, particulate and plankton fractions. Mercury processes included the input of atmospheric mercury, sedimentation, reduction, methylation and demethylation. The model simulations gave basically what were proper trends of the phenomena; quantitatively the measured and computed results are mainly within a factor of three. To simulate the non-uniform distribution of parameters over the depth, an existing three-dimensional (3D) hydrodynamic and transport-dispersion (TD) model, PCFLOW3D, was adapted and applied. As it was found that most mercury transport is related to suspended sediment particles, a new 3D sediment transport module was also developed and included in the model. Three cases are presented: one describing the simulation of TD of dissolved total mercury; another the simulation of the TD of particulate mercury in the Gulf during a river flood; and the third simulating sediment transport in the Gulf during a period of strong ENE wind. Comparison with measurements was only partly possible, but mainly the computed and measured results were within a factor of two and proper trends of the phenomena were obtained by the simulations. The combination of modelling and measurements has resulted in some interesting conclusions about the phenomenon of the transport and fate of mercury in a coastal sea.