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Groundwater depletion threatens many riparian ecosystems in arid and semiarid regions of the world. The aquifer that sustains Arizona’s San Pedro River riparian ecosystem, for example, is threatened by regional groundwater declines and localized pumping from the alluvial aquifer. This paper demonstrates the important role of shallow groundwater in structuring the San Pedro River plant community, portions of which function as reference areas that indicate site potential for a globally rare forest type (Sonoran riparian Populus-Salix forests). Several ecological indicators varied with depth to groundwater, including a weighted average wetland indicator score calculated for herbaceous and woody plant species, cover of plants within wetland indicator groups, and frequency of indicator plant species. These relationships can be used in a space-for-time substitution to predict consequences of groundwater decline. For example, the wetland indicator score changed sharply as depth to groundwater ranged from 0 to 4 m, and abundance of obligate wetland herbs (the group most sensitive to groundwater changes) declined sharply at groundwater depths below approximate to 0.25 m. Such sequential ’’desertification’’ of the riparian flora (i.e., loss or reduction in cover of species based on their probability of occurrence in wetlands) is one predicted response to groundwater decline. Other predicted impacts of groundwater decline include reduced establishment of Populus fremontii-Salix gooddingii forests, and reduced cover of herbaceous species associated with the fine-textured soils and shady conditions of floodplain terraces stabilized by these early seral tree species. High floodplain terraces (depth to groundwater of 5-8 m) had wetland indicator scores below those of upland sites and were vegetated by species (e.g., Prosopis velutina and Sporabolus wiightii) with low sensitivity to groundwater changes.