The birch wetland is an important type of oasis ecosystem in Xinjiang, China, which is extremely vulnerable to climate change and other disturbances. In this study, we aimed to understand the history of vegetation in such wetlands and find the key factors driving changes in the abundance of species inhabiting the wetlands of arid and semi-arid regions for over the past 900 years. Surface pollen samples were collected from 21 sites at altitudes between 750 m and 210 m, and 183 fossil samples were collected from the Ebinur and Caotanhu wetlands in north Xinjiang, China. Three different ground and surface water samples were collected from birch wetlands and the saline Ebinur Lake. The pollen and hydrochemical data were compared to examine the current interactions, and the knowledge thus gained was used to interpret historical changes in vegetation abundance in different regions (Ebinur and Caotanhu). The modern wetland landscape, surface pollen assemblage, and fossil pollen data from these areas together with hydrochemistry data concerning ground and surface water indicated that a local wetland ecosystem dominated by freshwater plants has been prevalent since 900 cal. a BP. The records show that Betula microphylla dominated the vegetation in the Caotanhu wetland from 900 to 700 cal. a BP; it subsequently declined and has now disappeared. In the Ebinur wetland, the vegetation cover of B. microphylla was at its highest between 270 and 220 cal. a BP; it is currently facing extirpation in the region. Our results, together with data concerning salinity and population statistics, indicate that both salinity and human activity have influenced wetland vegetation over the past 900 years. The two wetland ecosystems were dominated by freshwater plants during this period. At present, high salinity in the wetlands might be a key factor in driving the susceptible B. microphylla to extirpation. Increased human activity is an additional factor influencing changes in wetland vegetation. Overall, the results of our study on the interactions between wetland water and vegetation in different time periods (past and modern) and regions (Ebinur and Caotanhu) should be helpful for devising conservation strategies and conservation measures for B. microphylla in the semi-arid and arid areas of China.