Executive Summary. The Water Framework Directive (WFD) sets new standards for waters in the European Union. Classification systems will need to take into account the impacts of the physical modifications on riverine biota. Whilst there is a large literature on this subject, rigorous studies are difficult, because of the scale of the area impacted and the long-term nature of adjustment of biological systems. Nonetheless, a comparison of studies using in-stream, between stream, historical record and before-and-after methods show that river modifications, including changes to floodplain condition and connectivity alter the composition and abundance of riverine macrophytes, invertebrates and fish. River restoration schemes show varying success in restoring biological communities. This may be related to the continuing isolation of rivers from their floodplains, where floodplain habitat diversity plays an important role in maintaining ecological functions. Floodplain wetlands have a role to play in retaining nutrients and improving in-stream water quality. Both forests and grasslands have been shown to be effective in nutrient retention. A comparison of the River Great Ouse in England and the River Biebrza in Poland reveals that the hydro-morphological conditions of the Great Ouse have been dramatically altered in a manner that has demonstrable impacts on fish populations. Despite problems in identifying reference conditions and comparing complex dynamic systems, it is possible to conclude that the physical modification of rivers and their floodplains results in significant changes to biological communities. Fifteen per cent of lowland UK rivers are considered close to pristine, and a further 15% are considered semi-natural. This suggests that restoration is likely to be required on a large scale, to meet WFD requirements. Restoration should be based on an understanding of the processes that maintain biological communities, rather than focussing exclusively on improvements to channel condition. It should include reinstatement of natural flow regimes and flooding patterns and the creation of floodplain water bodies and side channels. Restoration of this kind, as well as contributing to the achievement of WFD objectives, would assist Government in meeting its obligations to wetland biodiversity, help to manage pollution and mitigate the impacts of flood and droughts, and provide opportunities for people to enjoy, and benefit from, rivers and their environs. 3 CONTENTS