Maintaining crop production levels with reductions in terrestrial greenhouse gases requires strategic residue and nitrogen (N) fertilizer management. Our objectives were to: (1) quantify the effect of nitrogen N application rate on N losses; (2) examine the role of residue returned on N transformation and losses; and (3) verify the capability of the NCSWAP/NCSOIL model to simulate the dynamics of N and 15N in the soil–plant system. Data obtained from a long-term continuous corn study on a silt loam soil, with two N levels (20 and 200 kg N/ha), with two types of residue management (residue harvested, −R; and residue returned, +R) was used to calibrate the model. The model accurately predicted 15N in the plant and soil organic matter (SOM) at the 0- to 15-cm and 15- to 30-cm depths for both fertilizer rates and residue managements. Concentrations of 15N in the corn and SOM were higher for the 20 than 200 kg N/ha treatments. Greater dilution of the 15N with nontracer fertilizer added at the higher fertilizer rate was responsible for differences in 15N concentrations in the plant. The predicted cumulative N loss during a 30-year simulation indicates more nitrate leaching past the 1-m depth for −R than +R treatments, while higher denitrification rates were predicted for the +R than −R. The simulated cumulative effect of residue returned on denitrification over 30 years predicted increased cumulative N losses from 1320 to 1705 kg N/ha and 1333 to 2574 kg N/ha for the low and high N application rates, respectively. Better synchronization of N release from residue and addition of N fertilizer with plant-N uptake would minimize leaching and denitrification.