A better understanding of how vegetation influences alluvial channels could improve (a) assessments of channel stability and flood risks, (b) applications of vegetation as a river management tool, and (c) predictions of channel responses to climate change and other human impacts. We take advantage of a natural field experiment in the semi-arid to arid Henry Mountains, Utah, USA: Large spatial differences in bed and bank vegetation are found along some alluvial channels due to localized perennial springs caused by aquicludes in the underlying bedrock. Airborne LiDAR topography and flood modeling are used to constrain channel morphology, vegetation density, and flow velocity at different flood discharges for three spring-fed reaches along intermittently-flowing streams. The spatial distribution of vegetation quantitatively influences both the magnitude and direction of channel adjustment. Reaches with abundant bed vegetation are significantly wider (by an average of ≈ 50%), with shallower flows and lower velocities, than reaches with little bed vegetation. Reaches with dense channel bank vegetation are ≈ 25% narrower and ≈ 25% deeper than sparsely-vegetated reaches. We interpret that sediment grain size influences the spatial distribution of vegetation within spring reaches, but that bank vegetation may be more important than grain size for “threshold” width adjustments. Widths, depths and velocities are fairly insensitive to whether local hydraulic roughness is parameterized in terms of local vegetation density or is assumed spatially constant, suggesting that the underlying “bare earth” topography of the channel bed, banks and floodplain exerts more control on local flow than does local vegetation density.