Continuously high flux of nitrogen (N) and phosphorus (P) input into rivers leading to water eutrophication has attracted public concern. The aim of the study was to determine the impact of N and P wet deposition on N and P transport in the forest watershed in Qianyanzhou, Jiangxi Province, China, based on the monitoring data from long-term sample and analysis. The results showed that from June 2013 to May 2014, the N and P wet deposition flux for the monitored watershed reached 11.86 kg/hm² and 0.38 kg/hm², respectively. There was a seasonal difference in deposition rates, wherein the N wet deposition mainly focus on the summer and autumn, accounting for 64% of total N wet deposition, whereas the P deposition mainly occurred in summer, accounting for 43% of total P wet deposition input. The pH fluctuation for watershed was large and the impact of land management (e.g., fertilizing) and rainfall events on N and P output were pronounced. The output of N and P mainly focus on the cultivation period, accounting for 96.2% and 61.4% of the total output from June 2013 to May 2014, respectively, which is because exogenous input of N and P from chemical fertilizers was large in this period. By analyzing the dynamic processes of N and P output during four rainfall events, we found that the impact of different intensities of rain events on the output process was different. The dilution effect on N and P output during rainfall process was significant before becoming runoff or rain intensity reached the storm level. Under heavy rain, P output was higher than that under other rainfall intensities. The contribution of N and P wet deposition to water were 101.97 kg and 0.60 kg, respectively. The N and P wet deposition in four rain events reached 4.46 kg and 0.032 kg, respectively, accounting for 15.22% of total N and 0.85% of total P output. According to the Eutrophication Index for the Xiangxi watershed, the water quality of the Xiangxi watershed is at moderate to severe degree of eutrophication state, especially during the cultivation period. We also analyzed that the N and P concentration in water during study period all exceeded the eutrophication threshold (N 1.5 mg/L, P 0.15 mg/L), which have the potential risk of water eutrophication.