Aquatic biodiversity has been declining at an alarming rate over the past decades as a result of increasing anthropogenic pressures on aquatic ecosystems. Freshwater Ecosystem-Based Management (EBM) consists of an integrated approach to ecosystem conservation and management that takes into account both the need to preserve and restore aquatic biodiversity and the necessity to ensure the current and future provision of ecosystem services for human populations. However, examples of EBM in freshwater ecosystems are rare. Ecohydrological models support EBM as they present a suitable and efficient tool allowing the assessment of not only the impact of global change but also the impact of regional and local changes on river ecosystems at different scales. Here, we present the application of an integrated, GIS-based model system that considers causalities from the catchment scale down to the reach scale and aquatic biota. It is based on the Driver-Pressure-State-Impact –Response (DPSI-R) concept and involves an ecohydrological model, 2 hydraulic models and a habitat model linked together. The prevailing macroinvertebrate community in the stream based on the river's substrates was modelled here. Results show good agreements between simulations and observations, for the physical parameters and also for the species occurrences. We discuss future requirements to extend the DPSI-R concept towards including ecosystem services as required for EBM.