The control of diffuse pollution requires information on the transport processes of those pollutants within a catchment. The characteristics of diffuse nitrogen and phosphorus discharged from a typical rural-agricultural catchment dominated by residential areas, sloping cropland, and forest land were monitored in the hilly area of the upper Yangtze River, China, and analyzed based on a total of eight rainfall-event runoff from August 2010 to September 2011. The results showed that the average of event mean concentrations (EMCs) of TN, DN, PN, TP, DP, and PP were 4.94, 3.18, 1.76, 1.11, 0.19, and 0.92 mg/L, respectively. The high EMCs demonstrated diffuse pollution of rural-agricultural catchment posing great pressure on receiving water. The first flush phenomenon for nitrogen and phosphorus was identified in rural-agricultural catchment, especially for the medium and heavy rainfall events, and a total of 36%, 44%, 46%, and 51% of the mass for TN, PN, TP, and PP, respectively, were discharged in the first 25% of the runoff. The first flush phenomenon suggested more attention should be paid on the management of the initial part of runoff in order to improve the efficiency of diffuse pollution control at catchment scale.