The Nanliujiang catchment is one of major rice production bases of South China. Irrigation districts play an important role in rice production which requires a large quantity of water. There are potential risks on future climate change in response to rice production, agricultural irrigation water use and pollution control locally. The SWAT model was used to quantify the yield and water footprint (WF) of rice in this catchment. A combined method of automatic and manual sub-basin delineation was used for the model setup in this work to reflect the differences between irrigation districts in yield and water use of rice. We validated our simulations against observed leaf area index, biomass and yield of rice, evapotranspiration and runoff. The outputs of three GCMs (GFDL-ESM2M, IPSL-CM5A-LR and HadGEM2-ES) under three RCPs (RCP2.6, 4.5, 8.5) were fed to the SWAT model. The results showed that: (a) the SWAT model is an ideal tool to simulate rice development as well as hydrology; (b) there would be increases in rice yield ranged from +1.4 to +10.6% under climate projections of GFDL-ESM2M and IPSL-CM5A-LR but slight decreases ranged from −3.5 to −0.8% under that of HadGEM2-ES; (c) the yield and WFs of rice displayed clear differences in the catchment, with a characteristic that high in the south and low in the north, mainly due to the differences in climatic conditions, soil quality and fertilization amount; (d) there would be a decrease by 45.5% in blue WF with an increase by 88.1% in green WF, which could provide favorable conditions to enlarge irrigated areas and take technical measures for improving green water use efficiency of irrigation districts; (e) a clear rise in future grey WF would present enormous challenges for the protection of water resources and environmental pollution control in this catchment. So it should be to improved nutrient management strategies for the agricultural non-point source pollution control in irrigation districts, especially for the Hongchaojiang and Hepu irrigation districts.
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