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The Middle Route of the South-to-North Water Diversion Project (MRP) is an important water supply for 20 large cities and 100 counties in Northern China. However, since 2016, the growth of large filamentous algae clusters has threatened the safety of the main canal water supply and water quality. In this study, a field investigation, monitoring, and hydrodynamic simulation were performed to analyze the hydrodynamic habitat conditions in areas with vigorous algae growth and establish a relationship between the hydrodynamic habitat conditions of the main canal and the growth, distribution, and correlation of macrobenthic algae in the main canal. The results showed that: (1) algae zones in the main canal are more likely to appear along curves, and the largest algal zone was at the front of the large curved section; (2) the length of the algae growth zone is related to the flow rate; and (3) a lower flow velocity in the main canal facilitates faster growth of an algae zone. This study provides specific and effective suggestions for the key prevention and control positions, which has important guidance on improving the efficiency of algae control in the main canal. [ABSTRACT FROM AUTHOR]