The increased frequency and intensity of heavy rainfall events due to climate change could potentially influence the movement of nutrients from land-based regions into recipient rivers. However, little information is available on how the rainfall affect nutrient dynamics in subtropical montane rivers with complex land use. This study conducted high-frequency monitoring to study the effects of rainfall on nutrients dynamics in an agricultural river draining to Lake Qiandaohu, a montane reservoir of southeast China. The results showed that riverine total nitrogen (TN) and total phosphorus (TP) concentrations increased continuously with increasing rainfall intensity, while TN:TP decreased. The heavy rainfall and rainstorm drove more than 30% of the annual N and P loading in only 5.20% of the total rainfall period, indicating that increased storm runoff is likely to exacerbate eutrophication in montane reservoirs. NO3−-N is the primary nitrogen form lost, while particulate phosphorus (PP) dominated phosphorus loss. The main source of N is cropland, and the main source of P is residential area. Spatially, forested watersheds have better drainage quality, while it is still a potential source of nonpoint pollution during rainfall events. TN and TP concentrations were significantly higher at sites dominated by cropland and residential area, indicating their substantial contributions to deteriorating river water quality. Temporally, TN and TP concentrations reached high values in May-August when rainfall was most intense, while they were lower in autumn and winter than that in spring and summer under the same rainfall intensities. The results emphasize the influence of rainfall-runoff and land use on dynamics of riverine N and P loads, providing guidance for nutrient load reduction planning for Lake Qiandaohu.