Ammonia surface flux is bidirectional; that is, net flux can be either upward or downward. In fertilized agricultural croplands and grasslands there is usually more emission than deposition especially in midday during warmer seasons. In North America, most of the ammonia emissions are from agriculture with a significant fraction of that coming from fertilizer. A new bidirectional ammonia flux modeling system has been developed in the Community Multiscale Air Quality (CMAQ) model, which has close linkages with the Environmental Policy Integrated Climate (EPIC) agricultural ecosystem model. Daily inputs from EPIC are used to calculate soil ammonia concentrations that are combined with air concentrations in CMAQ to calculate bidirectional surface flux. The model is evaluated against surface measurements of NH3 concentrations, NH4 + and SO4 2- aerosol concentrations, NH4 + wet deposition measurements, and satellite retrievals of NH3 concentrations. The evaluation shows significant improvement over the base model without bidirectional ammonia flux. Comparisons to monthly average satellite retrievals show similar spatial distribution with the highest ammonia concentrations in the Central Valley of California (CA), the Snake River valley in Idaho, and the western High Plains. In most areas the model underestimates, but in the Central Valley of CA, it generally overestimates ammonia concentration. Case study analyses indicate that modeled high fluxes of ammonia in CA are often caused by anomalous high soil ammonia loading from EPIC for particular crop types. While further improvements to parameterizations in EPIC and CMAQ are recommended, this system is a significant advance over previous ammonia bidirectional surface flux models.