Highlights: Human effects on ecological connectivity in aquatic ecosystems are reviewed. 40 Threats include: habitat loss, altered hydrology, invasive species, climate change. Case studies show improved understanding from multi-disciplinary approaches. Data on autecology, population structure, movement and physiology are critical. Planning requires data synthesis across life histories and temporal/spatial scales. AbstractUnderstanding the drivers and implications of anthropogenic disturbance of ecological connectivity is a key concern for the conservation of biodiversity and 50 ecosystem processes. Here, we review human activities that affect the movements and dispersal of aquatic organisms, including damming of rivers, river regulation, habitat loss and alteration, human-assisted dispersal of organisms and climate change.Using a series of case studies, we show that the insight needed to understand the nature and implications of connectivity, and to underpin conservation and 55 management, is best achieved via data synthesis from multiple analytical approaches.We identify four key knowledge requirements for progressing our understanding of the effects of anthropogenic impacts on ecological connectivity: autecology; population structure; movement characteristics; and environmental tolerance/phenotypic plasticity. Structuring empirical research around these four 60 broad data requirements, and using this information to parameterise appropriate models and develop management approaches, will allow for mitigation of the effects of anthropogenic disturbance on ecological connectivity in aquatic ecosystems.

1. Declaring protected areas (PAs) stands out as one of the main conservation strategies worldwide and there are clear commitments to expand their extent under the auspices of the Convention on Biological Diversity (CBD; Aichi targets for 2020). This conservation strategy has also received increasing attention in a freshwater context in the last two decades.2. Despite increasing conservation efforts, the effectiveness of PAs for freshwater purposes is questioned and freshwater biodiversity continues to decline. There are many reasons for this poor effectiveness: a lack of consideration of freshwater needs when designing and declaring protected areas, fewer resources devoted to freshwater conservation management than to other actions, and poor understanding of complex management problems beyond the limits of the protected area.3. This supplement compiles some examples from around the world on implementing and managing PAs, assessing their effectiveness, and demonstrating their important role not only in preserving biodiversity but also human well-being and in meeting future challenges to achieve the CBD targets for freshwater biodiversity.4. Here the challenges of establishing effective PAs for freshwater biodiversity in a rapidly changing world are reviewed. We advocate better monitoring programmes to assess the effectiveness of PAs for freshwater biodiversity, in which the unique characteristics of freshwater systems, such as the important role of connectivity and the close links with the rest of the landscape they drain, are considered.5. There are new conservation opportunities to enhance the value of PAs for freshwater biodiversity under the new conservation paradigm of 'people and nature'. The imperative of finding solutions that generate co-benefits alongside biodiversity conservation, and the clear reliance of human communities on freshwater services, has created an environment that may be more favourable to PAs focused in whole or part on fresh waters.

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