With rapid development of the Chinese economy in recent years, intensity of water resources development and utilization has increased significantly, leading to degradation of some water ecosystems. Assessment of the health status of river and lake ecosystems has therefore 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. In-depth research is done on physical morphology, hydrology and water resources, water environmental quality, and aquatic biological conditions. Principal component analysis, entropy method, and AHP hierarchical analysis are used, to establish a comprehensive evaluation system for water ecological health in Shandong province, and to conduct comprehensive evaluation of water ecological health of 12 typical river and lake water systems. The Shandong section of the Yellow River basin is found to maintain an overall healthy state, but some tributaries are sub-healthy due to insufficient ecological flow, dam construction, and damage to benthic organisms and macrophyte diversity. The overall health of the Nansi Lake basin is good, but Zhuzhaoxin River, Xinwanfu River, Guangfu River, and Baima River are sub-healthy due to natural shoreline damages, sediment pollutions, decreased diversity of macrobenthos and attached algae. Water ecological protection strategies are proposed hereinafter: to strengthen riverbank management, improve ecological flow protection mechanisms, control local sources of pollution. Construction of an efficient and scientific water ecological monitoring, evaluation, and management system is of great significance for promoting sustainable water resources utilization and ecological environment protection.