Abstract Background The extraction of water and alteration of flow regimes by humans have profound negative effects on river ecosystems. Returning water as “environmental flows” is a primary method for restoration, but evidence linking flow restoration to ecological benefits is weak. In order to draw more informative conclusions about the effects of environmental flows on ecosystems, reviews of ecological responses to altered flow regime need to focus on relationships between causes (flow components) and effects (ecological responses). We will review the literature on the responses of native riparian vegetation to flow alterations on regulated rivers. This review should improve river restoration efforts by identifying which flow components can be targeted by environmental flows to improve vegetation condition and increase abundance at the individual, population, and community levels. Methods We will conduct our review using the Eco Evidence framework, a novel, freely-available systematic review method and software that employs a standardised methodology to assess cause-effect hypotheses in the face of weak evidence. We will search published and grey literature for studies that present primary data on the responses of native riparian vegetation on lowland river banks to changes in flow regime. The review will assess evidence for seven distinct hypotheses that include different flow components (flood area, depth, duration, frequency, seasonality, and volume) and vegetation responses (condition, germination rates, reproduction, and survival). We will extract information from relevant studies on the trajectories of causes and effects, the type of study design, and the number of control and impact sampling units. This information will be used to weight studies, where studies with more sampling units or stronger study designs are given a higher weighting, as spurious results are less likely. The amount of weighted evidence supporting and refuting each hypothesis will determine which of four possible outcomes we will reach: “Support for hypothesis”, “Support for alternative hypothesis”, “Inconsistent evidence”, or “Insufficient evidence”. We will then collectively consider the conclusions for each hypothesis in order to answer our primary question, summarise the evidence, identify any gaps in knowledge, and provide recommendations for whether and how environmental flows could be used in the management of native riparian vegetation.