Riparian zones provide critical resources for wildlife, and are hotspots for biodiversity. Urbanization can affect biotic communities in riparian zones of urban areas by altering land cover of the surrounding landscape. However, shifts in communities may occur slowly, and there are few long-term studies in urban areas. The Central Arizona–Phoenix Long-Term Ecological Research (CAP LTER) program has been monitoring bird populations within the Phoenix metropolitan area and surrounding native Sonoran desert region since 2001. Monitoring sites include 12 riparian sites that span four habitat types featuring natural or engineered settings with perennial or ephemeral flows. Here, we used long-term data to address three questions: (1) How does bird species composition vary among riparian habitat types, (2) Which environmental variables explain variation in bird community composition and habitat characteristics of four riparian habitat types?, and (3) How has riparian bird community composition and abundance changed through time? Our analyses indicate that spring and winter communities have different migrant populations. Ephemeral habitat types support more desert-adapted bird species; whereas, perennial habitat types support more water associated species. Engineered habitat types support more urban-adapted bird species; whereas, natural habitat types support more specialists. Environmental variables at the site-level and landscape-level explained differences in habitat characteristics and bird community composition across riparian habitat types. Over time, bird communities at all habitat types decreased in abundance, species richness, and/or diversity. As contrasted with engineered habitat types, bird communities in natural settings changed more in species composition and had greater abundance decreases. Overall, the riparian bird community of the greater Phoenix metropolitan area is shifting toward more resident urban-adapted species that are characteristic of riparian areas with less water and more impervious surface.