Urbanization is frequently cited as a major driver of species losses worldwide; however, most studies in urban areas use a space-for-time substitution approach to document effects of urbanization through time. Ultimately, understanding the effects of urbanization on biodiversity requires long-term datasets. We examined long-term changes in bird assemblages at 12 riparian sites in the greater Phoenix metropolitan area and nearby Sonoran Desert region, featuring a range of human modifications and levels of water flow. Riparian areas in arid cities represent a key habitat type that is sensitive to human modification and supports high levels of species diversity. We used long-term data to: (1) explore variation in bird communities as a function of water permanence and degree of human-modification; (2) identify which environmental variables best describe differences found across riparian site types; and (3) assess how riparian bird communities, abundance, and species richness have changed through time. Engineered riparian sites supported more broadly distributed generalists; whereas, natural riparian sites supported more specialists. Sites with perennial flows had more vegetation and water compared to ephemeral sites and engineered sites had more impervious surface compared to natural sites. In nearly all comparisons, bird species richness, diversity, and abundance declined across riparian types during the period of study, even for common species. Bird communities in natural settings have changed more than communities at engineered sites. Overall, the riparian bird community is shifting toward urban dwelling, resident species that are characteristic of riparian sites with less water and more impervious surface.