Recently, a significant increase in macrophyte growth has been observed in many lowland rivers in Flanders, mainly due to eutrophication and an improvement of the water quality. This growth strongly influences the channel roughness (Manning-n). The first purpose of the project was a better understanding of the complex relationship between biomass development and discharge capacity in lowland rivers. In order to avoid the backing up of water upstream, the whole vegetation body is usually mowed annually. This project also investigated a lighter ecological management of aquatic plants in which only a part of the vegetation is removed in separate and alternating blocks, seeking a compromise between sufficient discharge and conserving large parts of the macrophyte vegetation with all its functions. Beside laboratory experiments, field survey was undertaken in the Grote Caliebeek, a tributary of the Kleine Nete in Flanders, Belgium. The results indicated that the presence of macrophytes in lowland rivers slowed down the waterflow and resulted in a raised water level. The upstream water level followed biomass development at a certain discharge level. The mowing experiments and the field survey indicated that alternating weed cutting patterns can reduce fall in an effective way. This research emphasizes the possibilities of alternating weed cutting patterns in order to deal with water flow problems. In the long term there will be the need for a better understanding of the ecological relationships in the search for a sustainable integrated method of controlling aquatic vegetation.