In desert regions, many streams have been dewatered due to anthropogenic water abstraction for agricultural and urban development. Other desert streams are transitioning from perennial to intermittent or ephemeral flow due to a drier and hotter climate. However, the discharge of treated wastewater (effluent) now has restored flow to some of those streams, recreating historic ecosystems and providing habitat for desert aquatic organisms. In 2019, effluent was used to restore flow in a historically perennial reach of the Santa Cruz River (Arizona, USA) that had been dewatered in the early 20th century. Although the flow restoration process was active, ecological restoration was passive, with species colonizing on their own rather than being transplanted. In this study, we documented community assembly across a two-year period in the Santa Cruz River following flow restoration. We also assessed the impacts of flow cessation, flooding, and urban flood channel maintenance (e.g. bulldozing, sediment removal) on aquatic invertebrate community structure. Colonization happened rapidly, especially for true fly, true bug, beetle, and dragonfly species. In total, we documented over 160 invertebrate taxa that had colonized the restored reach. Invertebrate taxa richness in the restored reach matched or exceeded that of a reference reach within 5 months. Flow cessation and channel maintenance events significantly reduced taxa richness and altered community composition, but flood events did not affect either of these metrics. However, even after two years, community composition had not converged in the restored and reference reaches, and many sensitive and poorly dispersing taxa have not yet colonized the restored reach. Overall, our results illustrate the great potential of tertiary-treated effluent in creating or restoring riverine habitats and supporting biodiversity in dewatered desert streams, but that assisted colonization may be necessary for some taxa.