Increasing human populations have resulted in aggressive water development in arid regions. This development typically results in altered stream flow regimes, reduced annual flow volumes, changes in fluvial disturbance regimes, changes in groundwater levels, and subsequent shifts in ecological patterns and processes. Balancing human demands for water with environmental requirements to maintain functioning ecosystems requires quantitative linkages between water in streams and ecosystem attributes. Streams in the Sonoran Desert provide important habitat for vertebrate species, including resident and migratory birds. Habitat structure, food, and nest‐building materials, which are concentrated in riparian areas, are provided directly or indirectly by vegetation. We measured riparian vegetation, groundwater and surface water, habitat structure, and bird occurrence along Cherry Creek, a perennial tributary of the Salt River in central Arizona, USA. The purpose of this work was to develop an integrated model of groundwater–vegetation–habitat structure and bird occurrence by: (1) characterizing structural and provisioning attributes of riparian vegetation through developing a bird habitat index (BHI), (2) validating the utility of our BHI through relating it to measured bird community composition, (3) determining the riparian plant species that best explain the variability in BHI, (4) developing predictive models that link important riparian species to fluvial disturbance and groundwater availability along an arid‐land stream, and (5) simulating the effects of changes in flow regime and groundwater levels and determining their consequences for riparian bird communities. Riparian forest and shrubland vegetation cover types were correctly classified in 83% of observations as a function of fluvial disturbance and depth to water table. Groundwater decline and decreased magnitude of fluvial disturbance caused significant shifts in riparian cover types from riparian forest to shrublands. Variability in the BHI was best explained by the cover of deciduous riparian tree species, primarily Populus fremontii, Platanus wrightii, and Salix gooddingii. The distributions of these plant species were well explained by the depth to groundwater and magnitude of fluvial disturbance along the stream. Bird species diversity and richness were significantly higher in sites with higher habitat indices. This quantitative linkage between surface and groundwater, plant species composition, habitat complexity, and bird communities has implications for water management and in determining environmental flows.

Nonnative Tamarix spp. (saltcedar) is among the most invasive and common trees along riparian habitats in the western U S, impacting native plant communities and habitat quality. Tamarix dominance causes a reduction in habitat physiognomic heterogeneity in riparian habitats. Animal abundance, diversity and habitat associations in monotypic stands of saltcedar remain largely unexplored for non‐avian communities. We sampled small vertebrate and ground arthropod communities in monotypic Tamarix stands and in mixed stands of Tamarix and native (Populus, Salix, and Prosopis spp.) trees in riparian habitats along the Virgin River in the Mojave Desert. Our survey of faunal communities suggests that many species of arthropods, reptiles and small mammals utilize both Tamarix‐dominated and mixed habitats along the Virgin River. Small mammal and lizard communities were dominated by generalist species. Mixed stands had greater arthropod abundance, lizard abundance and small mammal diversity; whereas, monotypic and mixed stands had similar lizard diversity. The habitat of mixed sites was characterized by ‘nativeness’ (areas with native riparian trees) and less ‘shady exotic thickets’ (areas with Tamarix and high overstory cover) compared to Tamarix‐dominated stands. There were species‐specific responses to habitat physiognomy. Peromyscus maniculatus (deer mouse) was associated with shady exotic thickets. Sceloporus magister (desert spiny lizard) and Neotoma lepida (desert woodrat) were associated with native trees and woody debris. Seven rodent and lizard species’ abundances were explained by habitat physiognomy variables. Rare and specialist species were more impacted by nonnative vegetation. These results contribute to the body of research on animal utilization of nonnative habitats and relation to habitat physiognomy. Management of nonnative plants should consider how control activities could impact habitat physiognomy and native animal communities in riparian habitat.