To address the need for systematic classification and quantitative identification of key nodes and functional channels in water networks, this study develops a comprehensive evaluation framework based on complex network theory. The framework integrates degree, betweenness centrality, and eigenvector centrality measures, and introduces a two-dimensional control-reachability matrix for identifying and classifying key nodes and functional channels within the water network structures of China’s four major river basins, including the Haihe River Basin, the Yellow River Basin, the Huaihe River Basin, and the Yangtze River Basin. The results indicate that the Huai River Basin has the highest proportion of core hub-type channels (22.02%), while the Hai River Basin shows significant polarization with 56.87% of nodes at higher grades. The proportion of medium transitional channels in the Yellow River Basin is as high as 88.10%, reflecting a balanced but weakly controlled structure. The proportion of marginally isolated channels in the Yangtze River Basin is 14.45%, indicating limited accessibility under complex terrain.