The Scaly-sided Merganser (SSME) is a globally endangered waterbird species, primarily inhabiting rivers. In recognition of its precarious status, it was added to the International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species in 2002. The SSME is highly sensitive to ecological environmental changes driven by changes in hydrological connectivity, particularly within riverine habitats. Changbai Mountain, a high-latitude water tower in the Northeast Asia, is considered one of the most optimal breeding grounds for the SSME worldwide. Its extensive water system and dense primary forest create an environment particularly well-suited for this species. Over the past 40 years, rivers within Changbai Mountain have experienced phases of hydropower development and ecological restoration. These activities have dramatically altered the hydrological connectivity of the area. However, the response of SSME to these changes in aquatic ecology, driven by shifts in hydrological connectivity, remains uncertain. We employed the AutoRegressive Integrated Moving Average (ARIMA) model to analyze changes in the population size of the SSME. Furthermore, the GeoDetector model was used to understand the impact of ecological changes on the maximum population size (MPS) and distribution of SSME in the context of alterations in hydrological connectivity. Our findings reveal that the restoration of hydrological connectivity, a method of ecological restoration, exerts a bidirectional influence on both the distribution and the MPS of SSME. Our findings can be summarized as follows. Firstly, there was a general trend of increase in both the distribution points and population size of the SSME. Secondly, the contribution of driving factors to the MPS of SSME was ranked in the following order: temperature > Connectivity Status Index (CSI) > river width > fish abundance > river depth > velocity > altitude > forest type. Thirdly, the impacts on the distribution and MPS of SSME were not due to a single factor, but rather a complex interplay of multiple factors. Finally, the construction of small hydropower stations significantly disrupted the hydrological connectivity of rivers, thereby altering the natural habitat of the SSME. The reduction in fish population, resulting from the loss of hydrological connectivity, adversely affected the MPS. Conversely, an increase in water temperature due to loss of hydrological connectivity positively impacted the MPS. However, these effects displayed heterogeneity across different rivers. Our study suggests that the construction of gravel dams may be a suitable approach in certain sections of the river, with a recommended height limit of 1.5 m. This research provides valuable insights for managers, offering a sustainable foundation for future energy planning and ecological restoration efforts.