The purpose of our approach was to take account of the nested scales of stream functioning on the links between pressures and ecological status by building and analysing a hierarchical model. The development of this model aimed at answering the following questions: Does the indirect links between pressures and ecological status modify the impact hierarchy of pressures? Do the different nested scales play a different role in the pressures-ecological status relationship? Does the model lead to better understanding of the specific role of hydromorphology in ecological status evaluation? To achieve that goal, we used the PLS path modelling method for developing a structural model linking the latent variables of (i) land use, and hydromorphological alterations at watershed scale, (ii) hydromorphological alterations at reach scale, (ii) nutrients-organic matter contamination levels, and (iv) substrate samples to explain macroinvertebrate based index I2M2 score variation. 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 result implies that hydromorphology has a major indirect effect on macroinvertebrates. And finally, the nutrients and organic matter effect on macroinvertebrates remains lower than expected since we take into account all the indirect effects of land use and hydromorphological alterations.