The basin of the Molenbeek is located in the province of East Flanders and flows through the municipalities of Zottegem (Godveerdegem, Erwetegem, and Grotenberge), Herzele (Herzele, Sint-Lievens-Esse, Woubrechtegem, and Ressegem), Haaltert (Heldergem, Kerksken, and Haaltert), Erpe-Mere (Aaigem, Mere, and Erpe) and Aalst (Aalst and Hofstade).
The Molenbeek is part of the Molenbeek Erpe-Mere drainage basin, which is itself part of the Dender basin.