The bacterial, acidobacterial, and fungal communities in wetlands can undergo perturbations by various human activities, such as disturbances caused by cultivation and during the process of system restoration. In this study, we investigated the relationships between the composition of the soil bacterial, acidobacterial, and fungal communities and the transformation of wetlands by human activities in the Sanjiang Plain. Soil microbial communities were assessed in wetland soils collected from pristine marsh, neighboring cropland (wetland turned into arable land), and land that had been reforested with Larix gmelinii. The alpha-diversities of bacteria, Acidobacteria, and fungi were affected by land-use change and were highest in the arable land and lowest in the wetland soils. The soil microbial community structures were also altered with changing land-use. Canonical correlation analyses showed that beta-diversity was significantly affected by soil pH, available phosphorus, soil nitrogen, and total organic carbon. Overall, our results showed that the agricultural cultivation of wetlands changes the available soil carbon, nitrogen, and phosphorus pools, thereby influencing the bacterial, acidobacterial, and fungal diversity and community structure. Once the soil microbial community has been altered by human activity, it might be difficult to restore it to its original state. These findings highlight the importance of effectively maintaining the diversity of soil bacterial, Acidobacterial, and fungal communities despite land use change in order to sustain a microbial community diversity and ecosystem function.