The atmospheric transport and fate of ammonia (NH3) depend on both meteorological and chemical conditions once it is emitted into the atmosphere. The largest source contributing to NH3 emission is the agricultural production, in particular animal operation, in North Carolina (NC). In this study, three-dimensional numerical meteorological and air quality models are applied to study the transport and fate of NH3 in the atmosphere in an area in southeast US centered over NC. One summer and one winter month simulations with a 4-km horizontal grid were conducted to simulate the meteorological and chemical environments for the transport and transformation of the reduced nitrogen, NHx ( = NH3 + NH4+) and to examine its seasonal variations and interactions with other chemical species (e.g., ozone and fine particular matter, PM2.5). The model performance for simulated meteorology and air quality was evaluated against observations in terms of spatial distributions, temporal variations, and statistical trends. MM5/CMAQ gave an overall good performance for meteorological variables and 03 mixing ratios and a reasonably good performance for PM2.5. The simulations show that 10-40% of total NH3 was converted to NH4+ at/near source and 40-100% downwind in August, and the conversion rates were 20-50% at/near source and 50-98% downwind in December. While the 3-D atmospheric models demonstrate some skills in capturing synoptic meteorological patterns, diurnal variations of concentrations of oxidants and PM2.5, and regional transport and transformation of NHx, reproducing meteorological and chemical features at a local scale and the magnitudes of hourly concentrations of oxidants and PM2.5 remain challenging due to uncertainties in model inputs and treatments. (c) 2007 Elsevier Ltd. All rights reserved.