Using tree-ring data of Pinus sylvestris var. mongolica from the Hulun Buir region in northeast China, 12 annual runoff series of the Hailar River spanning the past 202–216 years were established for the first time; these included 11 branches and one for the entire basin. These reconstructions, which could explain 29.4%–52.7% of the total variance for the measured runoffs during 1956–2006, performed well in statistical verification tests. In the whole basin’s reconstruction of 212 years, 34 extreme drought years (16.0%) and 41 extreme pluvial years (19.3%) were identified; 4 of the 10 most extreme years occurred after 1980. The consistent cycle and correlation revealed that the Hailar runoff had a teleconnection with the El Niño–Southern Oscillation (ENSO). The sharply increasing variance at the end of the reconstruction, accompanied by the increasing intensity of short cycles (4–8 years), indicated that runoff variability in the Hailar River basin has enhanced in the late twentieth century. This is verified by the drastic fluctuations in water level and area of rivers and lakes, and the frequent shift of natural land cover types in the Hulun Buir area in recent decades. The intensified runoff variability can be connected with the concurrently enhanced ENSO activity. Our study is the first to identify the intensification of recent runoff variability in the semiarid to arid region in northeast China from a long-term perspective. With projected enhancement of ENSO activity, the Hailar River basin will face the increased risk of extreme hydrological events.