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Background Rice paddy wetlands may serve as a nutrient source or sink in agricultural ecosystems. However, the pattern of nutrient loss on a watershed scale is not clear. A year-round on-site observation study based on 6-h intervals was conducted. Rainfall, temperature, runoff nutrient concentrations, and adjacent stream water samples were automatically monitored to uncover the temporal changes in the runoff losses of the predominant nutrient proxies (total N and total P) from a typical rice-planting area (120 ha) in the Yangtze river delta region of China. Results A high total N concentration in the rice-planting area was observed during the rice-planting season; however, significant fluctuation in the total P was evident throughout the year. The Δtotal N (drainage minus stream) parameter showed negative values with a mean of −0.25 mg L−1, while Δtotal P showed positive values with a mean of 0.06 mg L−1. The annual average N and P runoff from paddy field were 11.6 kg ha−1 and 1.5 kg ha−1, respectively. The window phases for the total N loss were mainly concentrated in the rice-growing season. However, the window phase for the total P loss was more dispersive throughout the year. No apparent relationships were found between rainfall and N and P concentrations by self-organizing map analysis. Conclusions The high-resolution monitoring, in this study, suggested that nutrient loss loading rather than nutrient concentration was strongly related to surface runoff Therefore, fertilization before high-intensity rainfall should be avoided to mitigate the nutrient runoff losses and maintain the rice wetland eco-function.