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Non-point source pollution is serious in the agriculture watershed of China. Understanding the characteristics of rainfall-runoff from agriculture watershed can provide theoretical support for controlling non-point source pollution. In this study, we investigated runoff characteristics of eight indices (dissolved total N, NO3--N, NH4+-N, total phosphorus, dissolved total phosphorus, particulate phosphorus, total organic carbon, COD) from three types of land uses, including farmland, forest and village in the downstream irrigation area of the Beiyunhe River basin. The results showed that the event mean concentrations (EMCs) of total dissolved N in village, farmland and forestland were 17.81 mg/L, 12.68 mg/L and 3.14 mg/L, respectively. EMC of total phosphorus in the order: farmland (0.44 mg/L) > village (0.22 mg/L) > forestland (0.17 mg/L). EMC of COD in the order: farmland (45.07 mg/L) > forestland (27.06 mg/L) > village (18.03 mg/L). The changes in the nutrients concentrations of the runoff water over a rainfall event indicated that the transports of the nutrients are similar among various land use types. The instantaneous concentrations of TN, NH4+-N, and NO3--N were high in the initial period of runoff, tend to decreasing with rainfall continuing, and increase in later period. Phosphorus concentration with time variation was not obvious among three land use types. The phosphorus species with high proportion in the total phosphorus was particle P (accounting for 75%) in forestland, dissolve P (79%) in farmland, and particle P (48%) and dissolve P (52%) in village. The curves of COD and TOC had been shown as high in the initial period of runoff, tending to increasing with rainfall continuing, and decrease in the later period. First-flush of all the indices were obvious in all three land use types with the rank of village > forestland > farmland. In village, all of the pollutions have taken place the phenomenon of first flush, while in farmland, pollutions tended to uniformly distribute or dilution throughout the storm event.