Fluxes of dissolved and particulate nitrogen (N) and phosphorus (P) variables were measured monthly from September 2007 to March 2009 in the upper Longchuanjiang River (Yunnan Province, China) to determine annual loads and seasonal variability. Dissolved N (DN) and particle associated P (PAP) contributed 56% and 99% of the total nitrogen (TN) and total phosphorus (TP) yields of 549 and 608 kg/km2/yr. Fluxes of particulate N (PN), dissolved P (DP), PAP and TP exhibited great seasonality because they were highly correlated with water discharge. Areal export rates of NH4–N, PN, PAP and TP were higher than in the main channel and most tributaries of the Changjiang River. High particulate loads were contributed to erosion of phosphorus-rich soils during heavily rains in the wet season. Median measured concentrations of TN, NH4–N and TP exceeded the maximum permissible limit for domestic and recreational use in China. High nitrogen and phosphorus concentrations draw attention to the potential for additional nutrient loading to foster the formation of algal blooms in locations where free-flowing river sections are changing into cascades of reservoirs. Importantly, the great seasonality in the data shows necessity of sufficient sampling for determining annual fluxes.