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Background: Cognitive and cerebrovascular declines are potentially life-changing conditions which are associated with a substantial healthcare burden worldwide. While pharmacological approaches for the prevention of cognitive decline have been largely ineffective, exercise programs may be able to delay or prevent cognitive decline in those at risk. One putative mechanism for the beneficial impacts of exercise on brain health involves improvement in cerebrovascular function. Exercise positively affects arterial structure and function in peripheral arteries and microvessels, but the impacts on brain vascular function are largely unknown. Water immersion increases brain blood flow and shear stress, a mechanism that improves artery health. We hypothesised that repeated water immersion may lead to adaptations which enhance cerebrovascular function and health in humans. Methods/design: 72 sedentary older adults (50 years and older) with subjective memory complaints were randomly assigned to a 24-week water-based or land-based walking program (designed to elicit differing stresses on blood vessels) or an education group. Measures of cerebral artery function and cognitive performance were assessed before and after the intervention, and again at 48 weeks to test for persistence of any benefits. Other outcomes included biochemistry, blood pressure, body composition and fitness. Discussion: Water-based versus land-based exercise elicit different haemodynamic responses and, consequently, distinct patterns of shear stress in arteries, including those supplying the brain. If the exercise programs prove beneficial, this will inform future strategies for the prevention of cerebrovascular decline in the ageing ‘healthy’ population.