Atmospheric deposition is among the largest pathways of nitrogen loading to the Chesapeake Bay Watershed (CBW). The interplay between future climate and emission changes in and around the CBW will likely shift the future nutrient deposition abundance and chemical regime (e.g., oxidized vs. reduced nitrogen). In this work, a Representative Concentration Pathway (RCP) from the Community Earth System Model is dynamically downscaled using the Weather Research and Forecasting (WRF) and Community Multiscale Air Quality (CMAQ) model coupled to the agro-economic Environmental Policy Integrated Climate (EPIC) model. The relative impacts of emission and climate changes on atmospheric nutrient deposition are explored for a recent historical period and a period centered on 2050. The projected regional emissions in CMAQ reflect current federal and state regulations, which use baseline and projected emission years 2011 and 2040, respectively. The historical simulations of 2-m temperature and precipitation have cool and dry biases, and temperature and precipitation are projected to both increase. Ammonium wet deposition agrees well with observations, but nitrate wet deposition is underpredicted. Climate and deposition changes increase simulated future ammonium fertilizer application. In the CBW at 2050, these changes (along with widespread decreases in anthropogenic nitrogen oxide and sulfur oxide emissions, and relatively constant NH3 emissions) decrease total nitrogen deposition by 21%, decrease annual average oxidized nitrogen deposition by 44%, and increase reduced nitrogen deposition by 10%. These results emphasize the importance of decreased anthropogenic emissions on the control of future nitrogen loading to the Chesapeake Bay in a changing climate.