The San Pedro River in southeastern Arizona is one of the last free-flowing rivers in the southwestern United States that maintains significant stretches of perennial water. While critical for birds, this river is vulnerable to salt cedar (tamarisk, Tamarix spp.) invasion, woody encroachment into grassland, and alteration of hydrologic regime resulting from groundwater pumping. Bird species richness and community composition metrics provide a means to assess effects of management or conservation efforts. To estimate these metrics, we used methods that incorporated species detection probabilities from data collected at 160 points at 23 sites on the San Pedro River during 1998–2001. Species richness, co-occurrence, and uniqueness were estimated as a function of four riparian vegetation types (cottonwood-willow [Populus-Salix], salt cedar, mesquite [Prosopis spp.], and grassland), three hydrologic regimes (perennial, intermittent, and ephemeral), and riparian location (floodplain and terrace). We found significantly higher species richness in cottonwood and mesquite compared with salt cedar and grassland. Intermittent and perennial flow sites had higher species richness compared with ephemeral. Cottonwood and mesquite supported more unique species compared with grassland and salt cedar, and cottonwood or perennial sites supported canopy or water-dependent species, for which habitat is rare on the landscape. Within the intermittent class, salt cedar maintained an estimated 0–2 unique species compared with native woody vegetation types, while cottonwood and mesquite contributed an estimated 20–21 unique species compared with salt cedar. Thus, while maintaining relatively high species richness, salt cedar contributed little to regional avian diversity compared with native woody riparian vegetation. This research has important implications for regional conservation planning and riparian restoration efforts.