The air quality has a key impact on the quality of life and human health. The atmospheric composition fields are formed as a result of complex interaction of processes with different temporal and spatial scales from global to regional to a chain of local scales. The earth surface heterogeneities, including the complex terrain, have a very significant impact on the atmospheric dynamics, hence on the formation of air pollution pattern. The incredible diversity of dynamic processes, the complex chemical transformations of the compounds and complex emission configuration together lead to the formation of a complex vertical structure of the atmospheric composition. The detailed analysis of this vertical structure with its temporal/spatial variability jointly with the atmospheric dynamics characteristics can enrich significantly the knowledge about the processes and mechanisms, which form air pollution, including near earth surface. The present paper presents some results of a study, which aims at performing reliable, comprehensive and detailed analysis of the atmospheric composition fields 3D structure and its connection with the processes, which lead to their formation. The numerical simulations of the vertical structure of atmospheric composition fields over Bulgaria have been performed using the US EPA Model-3 system as a modelling tool for 3D simulations and the system nesting capabilities were applied for downscaling the simulations from 81km to 9 km grid resolution over Bulgaria. The national emission inventory was used as an emission input for Bulgaria, while outside the country the emissions are from the TNO high resolution inventory.