We use an inorganic aerosol thermodynamic equilibrium model in a three-dimensional chemical transport model to understand the roles of ammonia chemistry and natural aerosols on the global distribution of aerosols. The thermodynamic equilibrium model partitions gas-phase precursors among modeled aerosol species self-consistently with ambient relative humidity and natural and anthropogenic aerosol emissions during the 1990s.Model simulations show that accounting for aerosol inorganic thermodynamic equilibrium, ammonia chemistry and dust and sea-salt aerosols improve agreement with observed SO4, NO3, and NH4 aerosols especially at North American sites. This study shows that the presence of sea salt, dust aerosol and ammonia chemistry significantly increases sulfate over polluted continental regions. In all regions and seasons, representation of ammonia chemistry is required to obtain reasonable agreement between modeled and observed sulfate and nitrate concentrations. Observed and modeled correlations of sulfate and nitrate with ammonium confirm that the sulfate and nitrate are strongly coupled with ammonium. SO4 concentrations over East China peak in winter, while North American SO4 peaks in summer. Seasonal variations of NO3 and SO4 are the same in East China. In North America, the seasonal variation is much stronger for NO3 than SO4 and peaks in winter.Natural sea salt and dust aerosol significantly alter the regional distributions of other aerosols in three main ways. First, they increase sulfate formation by 10–70% in polluted areas. Second, they increase modeled nitrate over oceans and reduce nitrate over Northern hemisphere continents. Third, they reduce ammonium formation over oceans and increase ammonium over Northern Hemisphere continents. Comparisons of SO4, NO3 and NH4 deposition between pre-industrial, present, and year 2100 scenarios show that the present NO3 and NH4 deposition are twice pre-industrial deposition and present SO4 deposition is almost five times pre-industrial deposition.