Multi-scale tracer and full-chemistry simulations with the STEM atmospheric chemistry model have been used to analyze the effects of both transported and local production of pollutants on California air quality during the ARCTAS-CARB experiment conducted in June 2008. During this summer experiment, simulated and observed O3 transport patterns from the coast to inland northern California are shown to vary based on the meteorological conditions and the oceanic O3 profiles, which are strongly episodically affected by Asian inflows. During a specific period, high coastal O3 air-masses at altitudes ~2-4 km can be transported inland and can significantly influence the surface O3 20-30 hours later over northern Sacramento valley, and the southern California can be indirectly affected by in-state transport. The model performance was improved by using LBCs downscaled from RAQMS global model that assimilated satellite data, as well as the LBC based on NASA DC-8 airborne observations during the experiment. The effects of SOx in these transported Asian air-masses over California were relatively less strong than O3 and its precursors, and the local emissions acted as the major contributor to the elevated sulfur concentrations below 5 km. Several SOx emission inventories (EI) were compared and the simulated SOx were validated with various observational datasets, with special focus on three regions - South Coast, San Francisco and Central Valley. The resolutions and the spatial and/or temporal variations of SOx emissions in all EIs remain to be further improved. Both terrestrial and maritime emissions were found important to coastal SOx distributions. Their percentile contributions to the coastal SOx spatial distributions for the experiment week were estimated, and the absolute contributions during flight periods were quantified. The California-Mexico atmosphere interaction majorly occurred between two sister city pairs-the coastal city pair (San Diego-Tijuana) was heavily affected by both California and Mexico maritime emissions through both directions. The effect was extended to the inland city pair (Mexicali-Calexico) by westerly winds, where was shortly impacted by southerly winds from Mexico, and limited areas over southeast of California were also affected.