Macrophytes were monitored in 48 headwater rivers in Flanders (Belgium). Only 26 sites had macrophyte vegetation, which was used to calculate five different indices and scores. These indices originated from UK, France, Czech Republic and Germany. Macrophytes were significantly correlated with a number of habitat variables, such as transect size, river width, slope, Huet zonation, distance to source, shadowing and average depth. For the substrate there were significant negative correlations with the fine particle sizes and a positive correlation with the coarse particles. A multivariate analysis of the macrophytes in these headwaters showed three groupings, essentially separated on basis of water hardness and pH.