Human activities such as agricultural fertilization and fossil fuel combustion have introduced a massive amount of anthropogenic nitrogen (N) in reactive forms to the environment. As agricultural fertilization is the single largest anthropogenic N source, an integrated approach to understand the interactions among agriculture, atmosphere, and hydrology is essential in examining human-altered N cycling. We have developed an integrated modeling system with agriculture EPIC, atmosphere WRF/CMAQ, and hydrology SWAT. This integrated system is useful tool for scientists and policy-makers to answer many questions on cycling of water, carbon, and nutrients for sustaining the food production while protecting the environment. This dataset is associated with the following publication: Ran, L., Y. Yuan, E. Cooter, V. Benson, J. Pleim, R. Wang, and J. Williams. An Integrated Agriculture, Atmosphere, and Hydrology Modeling System for Ecosystem Assessments. Journal of Advances in Modeling Earth Systems. John Wiley & Sons, Inc., Hoboken, NJ, USA, 11(12): 4645-4668, (2019).