Excess wet and dry deposition of nitrogen-containing compounds is a concern at a number of national parks. The Rocky Mountain Atmospheric Nitrogen and Sulfur Study (RoMANS) II campaign was conducted from November 2008 to November 2009 in order to characterize the atmospheric concentrations of sulfur and nitrogen species at Rocky Mountain National Park (RMNP), in north-central Colorado. The Comprehensive Air Quality Model with extensions (CAMx) is used to simulate the fate of gaseous and particulate species subjected to multiple chemical and physical processes for this study. This work presents a detailed operational model evaluation with special emphasis on the reduced nitrogen species measured during RoMANS II. The model emissions and meteorology are further examined as a result of the operational evaluation in order to improve the photochemical model predictions. The source apportionment of ammonia emissions is indirectly investigated with the Particulate Source Apportionment tool (PSAT) in CAMx and compared with source apportionment results from a “hybrid” approach using Empirical Orthogonal Function (EOF) analysis and a conservative tracer simulation.