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Agricultural systems in the U.S. Midwest have undergone rapid changes in atmospheric gradients of ambient nitrogen (N) deposition and carbon dioxide (CO2) concentration in recent decades. Despite potential impacts on soil-plant-atmospheric interactions, observed changes in these gradients have not been routinely considered in modeling studies, which could lead to biased results. This study evaluated the impacts of variation in nitrate concentration in rain water and ambient CO2 concentration on field-scale hydrology, nitrogen (N) dynamics, and crop yields in two tile-drained fields under a corn-soybean rotation in Illinois. A calibrated Root Zone Water Quality Model (RZWQM) coupled with Decision Support System for Agrotechnology Transfer (DSSAT) was used to simulate the impacts of ten scenarios over 10 years. Scenarios included a baseline with default values in RZWQM and each of the following three scenarios reflecting the actual changes for nitrate concentration (0.2, 0.3, and 0.4 mgN L-1), ambient CO2 concentration (360, 380, and 400 ppm), and combined effects (0.4 mgN L-1 and 360ppm, 0.3 mgN L-1 and 380 ppm, and 0.2 mgN L-1 and 400ppm). Nitrate concentration in rain water demonstrated a moderate impact on N dynamics (e.g. nitrate losses to tile drainage increased up to 5.8% compared to the baseline scenario), while it had a small impact on field-scale hydrology and crop yield. In contrast, increasing ambient CO2 concentration showed a significant impact on cropping system N dynamics and soybean yields (e.g. biological N fixation and soybean yields increased up to 29.1% and 24.6%, respectively, compared to the baseline scenario), whereas it had little impact on hydrology and corn yields. The combined effects scenarios showed that decreased nitrate concentration in rain water may partially be related to the slight improvements in water quality in Illinois during the last decades. Considering the recent changes in both nitrate and CO2 concentrations, the overall annual nitrate losses through water (i.e., nitrate losses in runoff, seepage, and tile drainage) decreased by 0.1 kgN ha(-1) and 1.3 kgN ha(-1) at two tile-drained fields. This study highlights the importance of proper consideration of atmospheric gradients in agricultural systems modeling procedure for accurately estimating crop productivity and environmental performance in tile-drained agricultural landscapes.