The Eastern Route of the South-to-North Water Diversion Project (ER-SNWDP) represents a crucial initiative aimed at alleviating water scarcity in China's northern region. Understanding the dynamics governing the composition and assembly processes of micro-eukaryotic communities within the canal during different water diversion periods holds paramount significance for the effective management of the ER-SNWDP. Our study systematically tracks the dynamics of the micro-eukaryotic community and its assembly processes along the 1045.4 km of canals and four impounded lakes, totaling 3455 km