Abstract: In recent years, with the rapid development of China's economy and society, the intensity of water resources development and utilization has significantly increased, leading to the degradation of some water ecosystems. Therefore, the assessment of the health of river and lake ecosystems has become a top priority in current water environment governance and protection efforts. This study focuses on the Yellow River and Nansi Lake basins in Shandong Province, conducting in-depth research on the physical morphology, hydrology and water resources, water environmental quality, and aquatic biological conditions of the rivers and lakes. By using methods such as principal component analysis, entropy method, and AHP hierarchical analysis, a comprehensive water ecological health evaluation system suitable for the actual situation in Shandong Province was established, and a comprehensive evaluation of the water ecological health of 12 typical river and lake water systems was conducted. The study revealed that the Shandong section of the Yellow River basin overall maintains a healthy state, but some tributaries of the Yellow River are in a sub-healthy state due to insufficient ecological flow, dam construction, and damage to benthic organisms and macrophyte diversity. Meanwhile, the overall health of the Nansi Lake basin is good, but areas such as Zuzhaoxin River, Xinwanfu River, Guangfu River, and Baima River are in a sub-healthy state due to problems such as natural shoreline damage, sediment pollution, and decreased diversity of macrobenthos and attached algae. Based on these findings, feasible water ecological protection strategies are proposed in this study, including strengthening riverbank management, improving ecological flow protection mechanisms, and effectively controlling local sources of pollution, aiming to enhance the health of the water ecosystems in Shandong Province. This research not only provides a scientific basis for regional water environment governance but also lays a solid foundation for the construction of an efficient and scientific water ecological monitoring, evaluation, and management system, which is of great significance for promoting sustainable water resources utilization and ecological environment protection.