The aim of this study is to quantify the physical alterations of alluvial rivers and reach a better understanding of the links between these alterations and the ecological quality of the river channels. This is an essential step towards river restorations, which are increasingly being considered in order to meet good ecological status as defined by the European Water Framework Directive. The methodology of this study involves comparing the ecological status of physically altered rivers to a reference model built from information obtained from about 30 non-altered sites in the chalky parts of the Seine Basin (northern France). The lengths of the studied sites are about 20 times the channel widths and the physical quality of the sites are determined using two adjustment parameters, the bankfull discharge and the hydraulic geometry. These are determined from topographical surveys and discharge measurements at two different discharges (one high and one low). The river substrate (sediment composition, size and transport) is also considered; as a control and adjustment parameter. A reference relationship between the bankfull discharge and different characteristics of the catchment (i.e. its size or annual discharge) are established. This allows auto-adjustments of streams in natural conditions to be evaluated and emphasises the morphological perturbations in channelised rivers (about 10 sites are studied). Biological data (mainly relative to fish populations) allow the structure of the communities in the reference rivers to be characterised and allow us to better understand when and how physical alterations induce modifications in the biocenoses.