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Drought-flood abrupt alternation (DFAA) is an extreme hydrological phenomenon caused by meteorological anomalies. To combat the climate change, the watershed integrated management modelSoil and Water Assessment Tool model (SWAT)was used to simulate DFAA, total nitrogen (TN) and total phosphorus (TP) from 1961 to 2050, based on measured precipitation data in the Hetao area and the downscaled Representative Concentration Pathways (RCPs) climate scenarios. In the future, the increase in temperature and the increase in extreme precipitation will aggravate the pollution of water bodies. Results indicate that the risk of water quality exceeding the standard will increase when DFAA happens, and the risk of water quality exceeding the standard was the greatest in the case of drought-to-flood events. Results also indicate that, against the backdrop of increasing temperature and increasing precipitation in the future, the frequency of long-cycle and short-cycle drought-flood abrupt alternation index (LDFAI, SDFAI) in the Hetao area will continue to decrease, and the number of DFAA situations will decrease. However, the zone of high-frequency DFAA situations will move westward from the eastern Ulansuhai Nur Lake, continuing to pose a risk of water quality deterioration in that region. These results could provide a basis for flood control, drought resistance and pollution control in the Hetao and other areas.