The use of nitrogen (N) fertilizer marked the start of modern agriculture that boosted food production to help alleviate food shortages across the globe but at the cost of severe environmental issues and critical stress to the agroecosystem. This paper was aimed at determining the fate and transport of nitrite and ammonia under future climate projections by adapting the recommended land management practices that are supposed to reduce nitrate N in surface water to state government target. To accomplish these objectives, a fully-distributed physical-based hydrologic model, MIKE SHE, and a hydrodynamic river model, MIKE 11, were coupled with MIKE ECO-Lab to simulate the fate and transport of different forms of N in the agro-ecosystem in the Upper Sangamon River Basin (USRB). Twelve (12) combinations of land management and climate projections were simulated to evaluate the N fate and transport in the USRB from 2020 to 2050. Under the current land management, the nitrate concentration in surface water was expected to exceed the EPA limit of 10 ppm up to 2.5% of the days in the simulation period. Regulating the fertilizer application rates to approximately 50% of the current rate will ensure this limit will not be exceeded in the future. Implementing cover cropping alone can potentially decrease nitrate N concentrations by 33% in surface water under dry climate and in the saturated zone under future projections. By combining the cover cropping and regulated application rate management, the nitrate N concentration in the saturated zone was expected to decrease by 67% compared with historic baseline. The modeling framework developed and used in this study can help evaluate the effectiveness of different management schemes aimed at reducing future nutrient load in our surface water and groundwater.