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.