The development of two comprehensive modelling systems and a test application to estimate the mercury budget for the State of New York is discussed in the present study. The modelling tools developed are based on two well known meteorological modelling systems namely, RAMS and SKIRON/Eta. Both models have been modified and the developed modules describing the physico-chemical processes of mercury have been incorporated in each modelling system. Model calculations and measurements have been compared during the 14 to 26 August 1997 simulation period. Two different simulations were performed, ‘scenario1’ where all available sources of mercury were used and ‘scenario2’ where the New York State mercury sources were excluded. An attempt was made to identify and quantify critical gaps in the current understanding of regional scale transport deposition and fate of mercury in New York State, improving modelling capabilities and understanding of mercury as an air pollutant, and provide a tool for policy makers in mitigating the impacts of mercury pollution.