The variation trends of precipitation, potential evapotranspiration, and runoff in the MRYR and nine sub-basins were analyzed by linear propensity estimation and the M–K trend test (Mann 1945). The results are shown in Figure 2 and Table 3. Precipitation in the five northern sub-basins (HF, KY, WD, YR, FR) is significantly less than that in the four southern sub-basins (BL, JR, YL, QR). The maximum annual precipitation (YL) is 1.6 times greater than the minimum annual precipitation (KY). Precipitation increases in the western sub-basins and decreases in the east. However, the potential evapotranspiration in the northern sub-basins is significantly larger than that in the southern sub-basins, indicating that the northern sub-basin is drier. Except for a significant decrease in precipitation in the QR (p < 0.01), all other basins showed a non-significant trend in precipitation. Potential evapotranspiration decreased significantly in HF (p < 0.05), YL, and QR (p < 0.01) and increased significantly in WD, FR, and BL (p < 0.01), while the trend was not significant in the other basins. Runoff in the nine sub-basins showed a significant decreasing trend (p < 0.01).