Vegetation cover and soil infiltration can result in nitrogen (N) redistribution and associative isotopic fractionation. This study investigated N and its isotopic characteristics from deposition to baseflow under different vegetation canopy cover types in a subtropical watershed in China. Results showed that canopy interception via vegetation cover types exhibited notable dilution effects on reactive nitrogen (Nr) deposition during the rainy season, with the highest maximum value of 287.4%. The range of δ15N changed from 3.0‰ to 11.9‰ in throughfall, which may have resulted from an increase in N taken up by vegetation and particles washed away from plant leaves during rainfall events. Throughfall, soil water, precipitation, and rainfall run‐off were the sources of D and 18O‐H2O in baseflow river water, wherein the rainwater and rainfall run‐off contributed 73% ± 8% and 15% ± 12%, respectively. Soil water was the main source of 15N‐NO3 in baseflow river water, which contributes 78% ± 4% of overall source, but precipitation only contributes 10%. The average annual Nr deposition flux was 24.4 ± 4.2 kg·ha−1·yr−1, whereas the annual total nitrogen exportation flux was 1062 ± 269.8 kg·yr−1. The 46% of HDO or D2O for river water came from rainfall run‐off, which would transport a maximum nitrate flux of 354 kg·yr−1. Moreover, vegetation cover and soil infiltration resulted in δ15N enrichment and a decrease in Nr in river flow.