peer reviewed ; In the present paper we investigated macrophyte community structure in 60 natural and impacted stream and river sites distributed throughout the Walloon river network. The objectives were to describe the distribution of macrophyte assemblages in relation to physico‐chemical parameters of their environment and to assess the variability in ecological metrics within these watercourses. Two‐way clustering allowed us to simultaneously assign sample units and species to groups by performing two separate cluster analyses. Indicator species analysis allowed us to assess the degree to which a species indicated a group, based on its constancy and distribution of abundance. Six end‐groups were identified as a result of using twoway clustering and indicator species analysis techniques. Hygroamblystegium fluviatile, Chiloscyphus polyanthos and Lemanea fluviatilis were found to characterize acidic and low impacted streams and rivers (G1), while Ranunculus fluitans was found in all low impacted large streams (G2). Potamogeton pectinatus, proved to be more common in eutrophicated waters in the calcareous areas particularly in the ʺLoess low plateauxʺ region (G6). Cinclidotus riparius, Fissidens crassipes and Pellia endiviifolia, appeared in rivers situated in the Condroz region (G4), which was characterized by a high concentration of nitrogen.