The high nitrogen load in most rivers across the globe causes various environmental issues. Non-point source (NPS) pollution within a watershed has a significant impact on water quality management and prediction accuracy in rivers. Temperature and streamflow, as the most important environmental indicators, significantly affect water pollution management. This study takes the Rappahannock River Basins (RRB) as a case and adopts the method of coupling land and river models to improve the simulation accuracy of river pollution, outputs and analyzes the temporal and spatial distributions of nitrogen pollution in RRB, assesses the impact of temperature and streamflow changes on nitrogen pollution in water bodies. The results show that NPS pollution is mainly affected by topography and land use, and the annual output is more correlated with the watershed area. Temperature is negatively correlated with NH4-N and NO3-N in the Rappahannock River. Nitrogen is more susceptible to streamflow in winter; but in summer, it was stable and even showed the opposite changing tendency to winter. Changes in temperature of 1.5 ∼ 2℃ and streamflow of 20 ∼ 50% have similar effects on NH4-N, while increasing streamflow can significantly increase the concentration of NO3-N, and most of these changes are very evident. NH4-N and NO3-N concentrations will increase in RRB when the summer temperature is below the long-term average. NH4-N concentration will increase when upstream streamflow (such as the amount of mountain snowmelt) decreases in winter, while NO3-N concentration will decrease. The establishment of the integrated model can provide the nitrogen pollution load of each sub-watershed and each segment, which can be used to develop the TMDL for the Rappahannock River.