•Annual nutrient losses of N/P values largely range from 0 to 20.•Key factors influencing N and P are latitude, precipitation and fertilizer.•Changes in N and P losses have resulted in a decline of N/P values.•N and P losses was generated according to SMC values for typical land use. Studies worldwide have indicated that agricultural pollution is the main source of nitrogen and phosphorus (N and P) in surface waters. A systematic understanding of N and P sources and sinks in agricultural systems is important for selecting the appropriate remedial strategies to control nutrient losses and water pollution. Based on nationwide data and a long-term monitoring program in Southeast China, the nationwide spatial and temporal patterns of N and P losses and the relationships between such losses and N and P inputs and rainfall were analyzed. The results showed that the annual nutrient losses from agricultural systems in China strongly varied, and the N/P values ranged from 0.01 to 51.0, with a majority at approximately 0–20, and an arithmetic mean of 9.73; these values mostly overlap the suitable range of N/P (6–15) for red bloom algae.