An approach for assessing the potential ecologic response of groundwater‐dependent riparian vegetation to flow alteration is developed, focusing on change to groundwater. Groundwater requirements for riparian vegetation are reviewed in conjunction with flow alteration statistics. Where flow alteration coincides with groundwater‐related vegetation sensitivities, scenarios are developed for groundwater simulation. Groundwater depths and recession rates in the riparian zone are simulated for baseline and altered stream hydrographs, with changes to river stage and width represented with a transient, flow‐dependent boundary condition. Potential flow diversion from the Upper Gila River in New Mexico is examined. Statistical flow alteration analysis, applying prospective diversions to a 76‐year record of daily flow, shows that flows in the winter‐spring months and within the high‐pulse to small flood range are subject to greatest potential change. Groundwater simulation scenarios are developed for these flow conditions in representative dry, near‐average, and wet years. Differences in groundwater elevations, generally less than 0.25 m during the flow alteration period, dissipate rapidly following cessation of diversion. Relating groundwater depth, recession rates and range of fluctuations to riparian vegetation needs, we find adverse ecological response is not expected from groundwater impacts for the flow alteration examined.