Watercourses are complex ecosystems where numerous economic, ecological and heritage issues converge. To ensure their efficient management it is essential to have a full description of these multifunctional ecosystems and to know their evolution over time. This paper describes a method for monitoring watercourses and their riparian strips developed in Wallonia (southern Belgium). It is based on an inventory constructed by stratified random sampling comprising 1,071 sampling plots distributed over a total length of 24,600 km of watercourses covered from their source. Each sampling plot is surveyed and measurements and fine observations are made on watercourse segments 50 m long. The method developed, which was applied on a regional scale, could easily be transposed to other entities, from large river basins, to an entire country. Examples of results obtained from a first inventory phase demonstrate the utility of this tool designed to supply qualitative and quantitative information to assist watercourse management.