The Riverstrahler model of ecological functioning of large drainage networks validated on the Seine river system has been used for calculating the seasonal variations of Production and Respiration at various spatial scales (e.g. according to river orders). Based on the measurements of biological processes, the P/R ratio has led to an evaluation of the "ecological functioning", beyond the notion of "good ecological status". Furthermore, the effects, on the P/R ratio, of the geomorphological and climate factors characterizing the Hydro-Eco-Regions (HER) of the Seine watershed have been quantitatively explored with the model. Whereas one finds a typical upstream-downstream pattern of the P/R ratio variations under the traditional rural conditions that prevailed in the Seine basin until the end of the 18th century, this pattern is strongly affected by the changes in urban populations and the implementation of wastewater collection and treatment, more than by the specificity of the physical factors characterizing the different HER. We have also found that autotrophy (a P/R ratio >1) might leads to eutrophication symptoms when P exceeds 1-2 mg C m(-2) d(-1) and that heterotrophy of the system (P/R ratio< 1) would reveal organic pollution when R exceeds 1-2 mg C m(-2) d(-1), stocks and fluxes of organic matter being expressed in carbon unit. Consequently, the P/R ratio appears as a good indicator of the perturbations caused by human activities in the watershed. The Riverstrahler model is able to quantify this effect.