Air quality models are increasingly used to develop estimates of dry and wet deposition of sulfate and nitrate in watersheds (because of lack of measurements) in an effort to determine the acidifying deposition load into the aquatic systems. These models need to be rigorously evaluated to ensure that one can rely on the modeled quantities instead of the measured quantities. In the United State (U.S.), these models have been proposed for use in establishing national standards based on modeled quantities. The U.S. Environmental Protection Agency (EPA) is considering aquatic acidification as the main ecological endpoint of concern in determining the secondary national ambient air quality standards for nitrogen oxides and sulfur oxides. Acidification is tied to depositions of sulfur and nitrogen, which are linked to ambient concentrations of the elements. As EPA proposes to use a chemical transport model in linking deposition to ambient concentration, it is important to investigate how the currently used chemical transport models perform in predicting depositions and ambient concentrations of relevant chemical species and quantify the variability in their estimates. In this study, several annual simulations by multiple chemical transport models for the entire continental U.S. domain are evaluated against available measurement data for depositions and ambient concentrations of sulfur oxides and reactive nitrogen species. The model performance results vary by evaluation time-scale and geographical region. Evaluation of annualized quantities (annual average ambient concentrations and annual total depositions) suppresses the large variances shown in the evaluation using the observation’s native shorter-term time-scales (e.g., weekly). In addition, there is a large degree of bias and error (especially for deposition fluxes) in the modeling results that brings to question the suitability of using air quality models to provide estimates of deposition loads. Variability in the ratio of deposition to ambient concentration, so-called the Transference Ratio that EPA has proposed to use in linking deposition to ambient concentration, is also examined. Our study shows that the Transference Ratios as well as total reduced nitrogen deposition, another modeled parameter EPA proposed to use in the process of determining the new secondary standard, vary considerably by geographical region and by model simulation.