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Purpose Endothelial dysfunction is an early and integral atherogenic event. Interventions that improve endothelial function also reduce cardiovascular risk. Due largely to the direct hemodynamic effects of repetitive exercise on the artery wall, exercise training has shown to enhance endothelial function. Land walking (LW) and water walking (WW) induce distinct hemodynamic responses, so the comparison of their effects provides an approach to study shear stress effects on endothelial function. We hypothesized that LW and WW training would have different effects on peripheral artery endothelial function. Methods Fifty-one sedentary, older (age = 61.9 ± 6.6 yr, 23.5% male) individuals were randomized into one of three groups: Control (n = 16), or one of two exercise groups consisting of 3 × 50 min supervised and individually tailored walking sessions per week for 24 consecutive weeks, performed either on LW (n = 17) or on WW (n = 18). Brachial artery endothelial function (flow-mediated dilation) and smooth muscle cell function (glyceryl trinitrate administration) were tested in all participants before (week 0) and after (week 24) the intervention. Results Differences were apparent in flow-mediated dilation change between the LW group (week 0, 5.39% ± 0.71%, to week 24, 7.77% ± 0.78%; P = 0.009) and the control group (week 0, 5.87% ± 0.73%, to week 24, 5.78% ± 0.78%). No differences in artery dilation response were found after glyceryl trinitrate administration (all P > 0.05). Conclusion This study suggests that 6-month center-based LW may be superior to WW in terms of improvement in arterial endothelial function in older sedentary individuals.