Abstract: The Yongding River serves as a critical water conservation area and an essential ecological barrier for the Beijing-Tianjin-Hebei region. Taking the Mentougou section of the Yongding River as the study area, this research integrated three categories of indicators—biology, water quality, and hydrology—to systematically assess the health status of the aquatic ecosystem. A rigorous indicator screening procedure was implemented: discrete analysis using the coefficient of variation (CV), contribution analysis using the CRITIC weighting method, and independence analysis using correlation tests (Spearman and Pearson). From an initial set of 17 candidate indicators, 10 core indicators were retained. The entropy weight method was then employed to determine the indicator weights, and a comprehensive water ecological health assessment system was established. Based on this system, the seasonal health status of 12 sampling sites was evaluated in both spring and autumn. The results reveal distinct spatial and seasonal differentiation patterns in the water ecological health of the Mentougou section of the Yongding River. Spatially, a clear ‘upstream better than downstream’ trend was observed. In the mountainous gorge section, most biological and hydrological indicators fell into the ‘good’ to ‘excellent’ grades. In contrast, the plain section—represented by sites such as Sanjiadian and the Yongding River Bridge—consistently showed lower comprehensive scores, which are closely associated with human disturbance. Seasonally, the overall health status in spring was better than that in autumn. The proportion of Level II (healthy) areas accounted for 41.7% in spring but declined to 33.3% in autumn. Specifically, biological indicators performed better in spring than in autumn, water quality indicators performed better in autumn, and hydrological indicators performed better in spring. Notably, the response of biological indicators to hydrological improvement exhibited a clear time lag, reflecting the nonlinear response characteristics of the aquatic ecosystem. Several typical sites further illustrated these patterns. At the Zhuwu Reservoir site, water quality and hydrological scores were high, yet biological scores remained relatively low. This phenomenon may be related to anthropogenic disturbance caused by dam construction, which alters natural flow regimes and reduces habitat suitability for benthic organisms. At the Wangpingcun site, the comprehensive evaluation was optimal in spring but declined sharply in autumn, likely due to the time-lag effect of ecological restoration projects and the impact of flood disturbance. At the Yongding River Bridge site, the comprehensive score remained the lowest among all sampling sites throughout both seasons. This indicates that while ecological water replenishment has achieved certain success in maintaining river flow, the overall ecological function has not yet been fully restored. Based on the above findings, differentiated ecological restoration strategies are proposed for the Mentougou section of the Yongding River. For the mountainous gorge section, priority should be given to protecting the integrity of natural habitats and maintaining natural hydrological rhythms. For the plain section, efforts should focus on strengthening ‘source control and pollution interception’ combined with ‘shoreline ecological reconstruction’. Moreover, ecological water replenishment should not only ensure adequate water volume but also simulate natural seasonal flow patterns to better support ecosystem recovery. This study provides a scientific basis for zoning management and ecological restoration of the Yongding River and offers a practical reference for water ecological health assessment in water-scarce urban rivers in northern China.