The interdisciplinary project “Resilient Rivers” links research in hydraulic engineering and ecology to explore processes and to evaluate measures related to river restoration. The partners from four different Swiss research institutions together with the Swiss Federal Office for the Environment are pursuing the common objective to develop scientific basics for answering current questions in restoration practice while involving experts from cantonal administrations, private offices and non-governmental organizations. The current project is the fifth phase within the Swiss national research program “Hydraulic Engineering and Ecology” which focusses on flood protection and functional riverscape habitats as well as current challenges such as biodiversity conservation, water use and adaptation to climate change. We introduce the 13 subprojects and highlight research questions, methodology, and collaboration. There are subprojects addressing lateral and longitudinal connectivity with regard to biodiversity of aquatic and terrestrial species, and connectivity will be studied locally at individual sites and on reach scale between different restoration sites. This includes also the study and modelling of hydrochory considering effect of sills and fluvial morphology, among others. Other subprojects are focusing on morphodynamics in river widenings, particularly with regard to sediment supply, flood protection and refuge availability, considering also climate change. Furthermore, instream structures such as engineered log jams are studied with respect to flood protection and habitat provision. The major common feature of all subprojects is the tight collaboration between hydraulic engineers and aquatic and terrestrial ecologists.