ABSTRACT The Holocene Rhine floodplain in Alsace, which represents a large homogeneity of petrographical regions, is used as a model for a comparative study of the interrelation of the different compartments (water-soil-plant) of two alluvial hydrosystems. We show that the species richness of alluvial forest, as well as the diversity of the ecosystems and the geoforms, are the main factors which explain the great efficiency in the functioning of the interfaces, e.g. retention on substrate, uptake and transformation of nutrients into biomass, and hence purification of the groundwater. We studied a canalized river deprived of a floodplain, the rapid transfer of eutrophicants and micropollutants in the canalized river itself and through the channel bed leads to a worsening of both surface and groundwater quality. By contrast a river with a functional floodplain provides large quantities of good quality water to the groundwater table. In this paper, we analyse the processes which occur at the interfaces of the different compartments.