Taking the nested scales of stream functioning into account in analysing the links between pressures and ecological status calls for the development of hierarchical models on the monitoring datasets. We aimed at answering the following questions: Does the indirect links between pressures and ecological status modify the classically observed impact hierarchy of pressures? Do the different nested scales play a different role in the pressures-ecological status relationship? Do hydromorphological alterations play a specific role in ecological status evaluation? To achieve that goal, we used the PLS path modelling method to develop a structural model linking latent variables built on (i) land use, and hydromorphological pressures descriptors at watershed scale, (ii) hydromorphological alterations assessed at reach scale, (ii) nutrients-organic matter contamination levels, and (iv) substrate samples to explain the score variation in the French monitoring macroinvertebrate based indicator I2M2. This method allows one to express the total effect of a variable as the sum of its direct and indirect effects. As a first important result, we have highlighted the importance of land use effect exerted on both hydromorphology and physico-chemistry and their translation as an indirect effect on biological condition of streams. We have also demonstrated that hydromorphological alterations had an effect on substrates structure and nutrients and organic matter concentrations. This study also reveals that hydromorphology has a major effect on macroinvertebrates indicator, thus indirect. Comparatively, nutrients and organic matter total effect on macroinvertebrates communities appears lower than expected since we take into account all the indirect effects of land use and hydromorphological alterations.