To reveal the impact of dry water encounter in different regions of the Yangtze River and Yellow River basins on the planning, design, and operation of national water network projects under changing environments, methods such as Copula function, spatial interpolation, cold and hot spot analysis, and SWAT model were used to reveal the spatiotemporal variation characteristics of dry water encounter probability in the two basins and future trends were analyzed. The results showed that the dry water encounter probability in the upstream Dajin-Lanzhou combination and Yajiang-Lanzhou combination significantly increased at a rate of 1.46% to 1.57% per 10 a, while Datong-Huayuankou combination significantly decreased at a rate of 1.04% per 10 a. The hot spots of Dajin Station and Yajiang Station were mainly located in the upper and middle reaches of the Yangtze River and the Yangtze River Delta region, while the cold spots were located in the “Ji shaped” bend of the Yellow River and the “two lake” area of the Yangtze River. The hotspots of Lanzhou Station and Huayuankou Station were located in south of the Loess Plateau in the middle reaches of the Yellow River, while the cold spots were concentrated in the middle and lower reaches of the Yangtze River. The multimodal average of dry water encounter probability in various station combinations in the future exceeds 20%. Among them, the Dajin-Lanzhou combination and Datong-Huayuankou combination showed a trend of first decreasing and then increasing, the Yajiang-Lanzhou combination showed a linear increasing trend, and the Huangjiagang-Huayuankou combination showed a trend of first decreasing and then slowly increasing.