Being one of the most important habitats for waterbirds, China’s West Songnen Plain has experienced substantial damage to its ecosystem, especially the loss and degradation of wetlands and grasslands due to anthropogenic disturbances and climate change. These occurrences have led to an obvious decrease in waterbird species and overall population size. Periodic and timely monitoring of changes in habitat suitability and understanding the potential driving factors for waterbirds are essential for maintaining regional ecological security. In this study, land cover changes from 2000 to 2015 in this eco-sensitive plain were examined using Landsat images and an object-based classification method. Four groups of environmental factors, including human disturbance, water situation, food availability, and shelter safety, characterized by remote sensing data were selected to develop a habitat suitability index (HSI) for assessing habitat suitability for waterbirds. HSI was further classified into four grades (optimum, good, general, and poor), and their spatiotemporal patterns were documented from 2000 to 2015. Our results revealed that cropland expansion and wetland shrinkage were the dominant land cover changes. Waterbird habitat areas in the optimum grade experienced a sharp decline by 7195 km2. The habitat area in good suitability experienced reduction at a change rate of −8.64%, from 38,672 km2 to 35,331 km2. In addition, waterbird habitats in the general and poor grades increased overall by 10.31%. More specifically, the total habitat areas with optimum suitable grade, in five national nature reserves over the study region, decreased by 12.21%, while habitat areas with poor suitable grade increased by 3.89%. Changes in habitat suitability could be largely attributed to the increase in human disturbance, including agricultural cultivation from wetlands and grasslands and the expansion of built-up lands. Our findings indicate that additional attention should be directed towards reducing human impact on habitat suitability for sustainable ecosystems.