Human appropriation of water resources may induce water stress in freshwater ecosystems when ecosystem needs are not met. Intensive abstraction and regulation cause river ecosystems to shift towards non-natural flow regimes, which might have implications for their water quality, biological structure and functioning. We performed a meta-analysis of published studies to assess the potential effects of water stress on nutrients, microcontaminants, biological communities (bacteria, algae, invertebrates and fish), and ecosystem functions (organic matter breakdown, gross primary production and respiration). Despite the different nature of the flow regime changes, our meta-analysis showed significant effects of human-driven water stress, such as significant increases in algal biomass and metabolism and reduced invertebrate richness, abundance and density and organic matter decomposition. Water stress also significantly decreased phosphate concentration and increased the concentration of pharmaceutical compounds. The magnitude of significant effects was dependent on climate, rainfall regime, period of the year, river size and type of water stress. Among the different causes of water stress, flow regulation by dams produced the strongest effects, followed by water abstraction and channelization.