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Summary: The effect of future climate scenarios on surface water and groundwater resources has been shown to have a consequent impact on water-dependent ecosystems. A regional-scale analysis of changes in water resources as a result of changing climate was undertaken in south-western Australia; a region with a large number of nationally and internationally recognised water-dependent ecosystems. The paper examines the potential environmental impacts of a substantial reduction in rainfall and an increase in temperature as projected by global climate models (GCMs) on river and groundwater-dependent terrestrial vegetation by 2030. Climate change effects on environmentally significant flow regimes were evaluated by applying the climate projections from 15 GCMs under three global warming ‘scenarios to rainfall–runoff and groundwater models. It was estimated that under a dry future climate scenario, the frequency of river flow rates important for ecological communities is likely to be reduced by up to 2months per year, which is likely to cause a significant level of stress to ecological communities. Additionally, the duration of no-flow periods may increase by more than 120days in some streams. Under a dry future climate scenario, groundwater-dependent vegetation is projected to be at a high risk in over 19% of its current habitat area. Water-dependent ecosystems are also projected to be affected by an increase in groundwater abstraction. The results indicate that the projected impacts of future climate conditions are not likely to be uniform across the region but overall they could cause a continuing threat to water-dependent ecosystems. The implementation of water management plans should place particular emphasis on the ecological water requirements in 6 of the 13 river catchments in south-western Australia and in areas where groundwater abstraction is high. The climate projections and ecological impacts are a continuation of the trends that have taken place in the past three decades. [Copyright &y& Elsevier]