Runoff variation in the Wuyur River catchments and its influence on the succession of the Zhalong saline marsh were analyzed using Mann-Kendall test and moving t-test method. The results indicated that rapid degradation of the marsh was closely correlated with the runoff amount variation in Wuyur River Catchment. The runoff entering the wetland was significantly decreased since 1980s, i.e., the runoffs decreased from 8×108 m3 in 1960s to less than 3×108 m3 in 21st century, with the lowest 1×108 m3. Runoff amount decreasing in Wuyur River catchments resulted in sustained drought and water shortage in Zhalong Wetland, and thereby induced to water quality severe deteriation and large area of marsh disappear. For example, the area of saline soil significantly increased from 150 km2 in 1979 to 245 km2 in 2015 in the Zhalong wetland. Most water body in the wetland reached a level of eutrophication status, even to be severe rich level in some areas, and the water in the wetland is generally getting worse. Long-term drought would impair the ecological function of the Zhalong wetland and even impact on the ecological safety of the whole western region of Songnen Plain.