Groundwater is a key driver of riparian condition on dryland rivers but is in high demand for municipal, industrial, and agricultural uses. Approaches are needed to guide decisions that balance human water needs while conserving riparian ecosystems. We developed a space‐for‐time substitution model that links groundwater change scenarios implemented within a Decision Support System (DSS) with proportions of floodplain vegetation types and abundances of breeding and migratory birds along the upper San Pedro River, AZ, USA. We investigated nine scenarios ranging from groundwater depletion to recharge. In groundwater decline scenarios, relative proportions of tall‐canopied obligate phreatophytes (Populus/Salix, cottonwood/willow) on the floodplain progressively decline, and shrubbier species less dependent on permanent water sources (e.g. Tamarix spp., saltcedar) increase. These scenarios result in broad shifts in the composition of the breeding bird community, with canopy‐nesting and water‐obligate birds declining but midstory nesting birds increasing in abundance as groundwater declines. For the most extreme draw‐down scenario where all reaches undergo groundwater declines, models project that only 10% of the upper San Pedro floodplain would be comprised of cottonwood/willow (73% saltcedar and 18% mesquite), and abundances of canopy‐nesting, water‐obligate, and spring migrant birds would decline 48%, 72%, and 40%, respectively. Groundwater recharge scenarios were associated with increases in canopy‐nesting birds particularly given the extreme recharge scenario (all reaches regain shallow water tables and perennial streamflow). Model outputs serve to assess the sensitivity of biotic groups to potential changes in groundwater and thus to rank scenarios based on their expected ecological impacts.