The programme LIFE Nature "Conservation and restoration of habitats of the Rhine fringe" (2002-2005) focussed on the assessment of the conservation status of terrestrial and aquatic habitats. Along the Rhine fringe, the degree of connection between waterbodies and the river main channel determined the water flow (surface or phreatic waters, flow velocity) and induced flood disturbances (hydromorphological quality, scouring effect). A new typology based on metrics characterizing the conservation status, was proposed for the upper Rhine floodplain. Seven physical and biological metrics were selected: specific richness, presence or absence of rare, polluto-tolerant and exotic species, species abundance, degree of connection, and trophy level defined by the macrophyte community. Aquatic macrophytes surveys were conducted at 315 sites along the Rhine French fringe. Multiple correspondence analysis and discriminant analysis were used to define metrics scores in a preliminary network of 129 macrophytes surveys stands. Metrics were combined to give a measure of the conservation status of the 315 sites. Five classes of the conservation status have been defined from degraded to excellent status. The mapping of the conservation status was realized to answer the question addressed by the program “Life Nature”. We discuss on the choice of the metrics and their justification in the definition of the conservation status. The method was tested in the fluvial hydrosystem of Ill river, the main tributary of the Rhine river in the Alsace floodplain, and compared to the French trophic index based on macrophytes, IBMR.