Atmospheric deposition of nitrogen (N) is a major contributor to eutrophication of estuarine and coastal waters. It is estimated to contribute 20-35% of the N load to east coast and gulf coast estuaries in the United States. Most of the N loading is contributed indirectly by first depositing on the watershed. Currently, oxidized-N from nitrogen oxide (NOx) emissions from combustion is the major source of N in total (wet + dry) atmospheric deposition. With the anticipated control of NOx emissions, to reduce ozone, model projections suggest that reduced-N from ammonia (NH3) emissions will become the major source of atmospheric N deposition in the future. Agriculture is by far the largest contributor to ammonia emissions. In some disciplinary areas the conventional wisdom is that all of the NH3 emissions deposit locally, an idea that is not consistent with what we know in the atmospheric community. Initial ammonia budget studies of an emissions hot spot and an emissions region with a regional atmospheric model, EPA's Community Multi-scale Air Quality Model (CMAQ) show that while local deposition is significant in the vicinity of NH3 emission regions, a majority of the emissions loft up into the atmosphere away from the surface, are converted to aerosol ammonium and subsequently subject to long-range transport. Close to the source dry deposition dominates and farther from the source wet deposition dominates. Additional budget studies are developed to address how uncertainty in the NH3 dry deposition rate affects the uncertainty in the long-range transport and regional influence of ammonia emissions. A major source of uncertainty related to ammonia deposition is the empirical observation that ammonia flux is really bi-directional. A preliminary bi-directional parameterization has been included in CMAQ. One of the budget studies examines the impact of this bi-directional formulation of ammonia air-surface exchange on long-range transport of ammonia emissions.