The flow regime is a key driver of river and floodplain wetland ecosystems. This review highlights four principles linking hydrology and aquatic biodiversity, and the impacts of altered flow regimes. First, flow determines physical habitat in streams, which in turn determines biotic composition. Second, aquatic species have evolved life history strategies in response to natural flow regimes. Third, maintaining natural patterns of longitudinal and lateral connectivity is essential for the viability of riverine species. Fourth, altered flow regimes facilitate the invasion and success of exotic species. Flow influences stream habitats at multiple scales, affecting channel dimensions, riffle-pool distribution, and hydraulic conditions. These habitat changes influence the distribution and abundance of aquatic organisms. Flow patterns shape life history strategies of aquatic species, and altered flow regimes can lead to recruitment failure and loss of native biodiversity. Maintaining natural connectivity is crucial for population viability, as barriers disrupt movement and lead to isolation, failed recruitment, and local extinction. Exotic species are more likely to succeed in modified flow regimes, as they are adapted to these changes. Flow regimes influence aquatic biodiversity through various mechanisms, including channel form, habitat availability, and life history patterns. Changes in flow regimes due to land-use and water resource development can lead to declines in biodiversity. The invasion of exotic species is facilitated by altered flow regimes, and interbasin water transfers are a major mechanism for their spread. Current understanding is based on untested hypotheses, and further research is needed to predict and quantify biotic responses to altered flow regimes. Aquatic science should move towards experimental and manipulative studies to better understand these impacts and guide restoration efforts.The flow regime is a key driver of river and floodplain wetland ecosystems. This review highlights four principles linking hydrology and aquatic biodiversity, and the impacts of altered flow regimes. First, flow determines physical habitat in streams, which in turn determines biotic composition. Second, aquatic species have evolved life history strategies in response to natural flow regimes. Third, maintaining natural patterns of longitudinal and lateral connectivity is essential for the viability of riverine species. Fourth, altered flow regimes facilitate the invasion and success of exotic species. Flow influences stream habitats at multiple scales, affecting channel dimensions, riffle-pool distribution, and hydraulic conditions. These habitat changes influence the distribution and abundance of aquatic organisms. Flow patterns shape life history strategies of aquatic species, and altered flow regimes can lead to recruitment failure and loss of native biodiversity. Maintaining natural connectivity is crucial for population viability, as barriers disrupt movement and lead to isolation, failed recruitment, and local extinction. Exotic species are more likely to succeed in modified flow regimes, as they are adapted to these changes. Flow regimes influence aquatic biodiversity through various mechanisms, including channel form, habitat availability, and life history patterns. Changes in flow regimes due to land-use and water resource development can lead to declines in biodiversity. The invasion of exotic species is facilitated by altered flow regimes, and interbasin water transfers are a major mechanism for their spread. Current understanding is based on untested hypotheses, and further research is needed to predict and quantify biotic responses to altered flow regimes. Aquatic science should move towards experimental and manipulative studies to better understand these impacts and guide restoration efforts.