In this study, three typical peat cores were collected from Tuqiang(TQ) of Great Hinggan Mountain, Youhao (YH) of Small Hinggan Mountain and Honghe(HH) of Sanjiang Plain wetlands, in the upper, middle and lower streams of Heilongjiang River basin (HRB) of Northeast China. The peat cores were around 50 cm in length and were dated back 100 years by ~(210)Pb and ~(137)Cs techniques. A high-resolution analysis of testate amoebae was conducted using a sieving procedure with Lycopodium spore addition. Based on a built paleohydrology transfer function in Northeast China, the 100-year history of water level change was reconstructed in HRB wetlands, and the possible affecting factors were also discussed. Results showed that the ages of the TQ, YH and HH cores covered the time scale of the Anthropocene. In the different areas of the upper, middle and lower streams, there were significant spatial differences in the testate amoebae species. The constrained clustering results showed that the history of water level change in HRB wetlands could be divided to three periods : 1) the early Anthropocene (approximately 1915), the wetland habitat was relatively humid and the testate amoebae were dominant with the "humid" species, e.g., Heleopera petricola/sphagni,Hyalosphenia papilio. However, the depth to water table (DWT) gradually increased, indicating a drought trend of the wetland habitat. In this period, the regional climate change would be the controlling factor of wetland water table. 2) During 1915 ~ 1990,the variations of wetland water levels showed significant difference in the upper, middle and lower streams. At TQ wetland, the decreasing DWT indicated an increasing humid habitat, and the "humid" species like Hyalosphenia papilio and Centropyxis aculeata type increased. However, at YH and HH wetlands, the DWT increased and the habitat became drier. The humid" species significantly decreased and the arid" species including Phryganella acropodia, Trigonopyxis arcula, Assulina muscorum increased. Due to the weak anthropogenic influence, the regional climate change was still the main driver to the water table variation in TQ and YH wetlands. The significant influence of human activities would be the main driver to the water table variation in HH wetland. 3) Since 1990,there was an increasing anthropogenic impacts on the water table change throughout the HRB wetlands. The DWT increased in the upper and middle streams, indicating a drying habitat in TQ and YH wetlands. The dominant species of testate amoebae were Phryganella acropodia, Assulina muscorum and Assulina seminulum. In HH wetland, the DWT became lower, probably due to the input of agricultural excess irrigation. In the past century, the water table change in HRB wetlands was controlled by regional climate change and the human being's activities, and suggested a significant spatial difference in the upper, middle and lower streams.