In the town of Idrija, Slovenia, the world's second largest mercury mine was active for 500 years and about 37,000 tons of mercury has been lost in the environment. Mercury is still drained from soil, riverbed and floodplains and transported with the Idrijca and Soca Rivers to the Gulf of Trieste. A part of inorganic mercury is methylated either in the river system, or later in the coastal area, and, due to its bioaccumulation and biomagnification represents potential danger to human health. A 1-D aquatic model MeRiMod was used to simulate hydrodynamics and sediment transport in the river system from Idrija to the Soca River mouth. Transport of particle bound and dissolved mercury as well as potential net methylation of mercury in the river system was simulated. The simulation of an observed flood wave with 20-year recurrence period was performed in order to validate the model. Methylation was simulated at lower discharges, as higher methylation rates occur in such conditions. The measurement data and the MeRiMod model were also used to establish a historical mercury mass balance of the Idrijca and Soca Rivers catchment. Sediment core data from the Gulf of Trieste and the measured concentrations from floodplains were used to verify and calibrate the model. Simulations of different high discharges were performed as most of the transport of particulate mercury occurs within flood wave conditions. Compared to the measurements, the results of the model showed an agreement within an order of magnitude, for the transport of total mercury mostly within a factor of 4, and for the methylation within a factor of 5. However, proper trends of the phenomena were obtained by simulations. The combination of modelling and measurements has resulted in some interesting conclusions about the phenomenon of the transport and transformations of mercury in the observed river system.