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The combined UAM-AERO/RAMS modeling system has been applied to study the dynamics of photochemical gaseous species and particulate matter processes in the eastern Mediterranean area between the Greek mainland and the island of Crete. In particular, the modeling system is applied to simulate atmospheric conditions for two periods, i.e., 13–16 July 2000 and 26–30 July 2000. The spatial and temporal distributions of both gaseous and particulate matter pollutants have been extensively studied together with the identification of major emission sources in the area. New pre-processors were developed for the UAM-AERO model for evaluating detailed emission inventories for biogenic compounds, resuspended dust and sea salt. Comparison of the modeling results with measured data was performed and satisfactory agreement was found for a number of gaseous species. However, the model underestimates the PM10 measured concentrations during summer. This is mainly due to the considerable underestimation of particulate matter emissions and in particular dust resuspension, the effect of forest fire emissions and the contribution of Saharan dust episodes.