Anthropogenic degradation of aquatic ecosystems—rivers, lakes, estuaries and coastal waters— is manifold, pervasive and dates back for centuries in Europe. The ecosystems are affected by physical, chemical, hydrological and morphological modifications, all of which impose environmental pressures on the structure and function of aquatic communities. Human impacts on aquatic ecology have frequently been studies and numerous indicators for assessment and monitoring of various environmental impacts on aquatic ecosystems were developed. In response, the knowledge about the linkages between environmental pressures and aquatic communities was used to derive appropriate measures to rehabilitate and restore aquatic ecosystems. Restoration ecology is often assuming that communities are beginning to recover as soon as the pressures are reduced or removed. However, the simple reversal of degradation equally often does not show the desired and anticipated ecological effect and the biota continue to stay ‘degraded’. Firstly, the small spatial scale of many restoration measures does not fit the often very broad-scale degradation at the catchment level; secondly monitoring activities are rather short-term and do not sufficiently account for long time periods required for restoration; and thirdly, the knowledge about a catchment’s potential for recovery is sparse. This report on Conceptual Modelling of restoration and recovery presents a framework to summarize and structure the current knowledge on the effectiveness of river restoration measures and its impacts on the in-stream plant and animal communities. The Conceptual Models are used to illustrate the relationships between three common restoration measures, its effects on instream environmental key variables and the impact of the changing variables on benthic algae, macrophytes, benthic invertebrates and fish. The restoration measures are: i) instalment of riparian buffers to improve water and habitat quality, ii) placement of in-stream structures to improve the mesohabitat and iii) removal of weirs to restore connectivity, hydrology and geomorphology. The Conceptual Models are used to identify well-known cause-effect chains for restoration, but also knowledge gaps based on the peer-reviewed scientific literature and amended by selected reports from the grey literature.