Freshwater and riparian ecosystems are tightly coupled by the flow of resource subsidies across aquatic and terrestrial boundaries, yet highly vulnerable to the environmental stressors associated with urban expansion. Ongoing declines in insectivorous and migratory bird populations are attributed in part to parallel reductions in riparian habitat and the availability of aquatic and terrestrial prey. However, our understanding of how anthropogenic stressors alter aquatic resource subsidies, and how these changes propagate to avian consumers, remains limited. Leveraging benthic macroinvertebrate surveys and avian acoustic monitoring data from streams spanning an urbanization gradient in the Seattle metropolitan area of Washington, USA, we use multi-species occupancy and structural equation modeling to disentangle the effects of biotic and abiotic factors on the diversity of birds and their aquatic insect prey during the breeding season. We found that a benthic index of biotic integrity (B-IBI) strongly influenced both the occupancy and richness of invertivorous predator and migrant guilds, more so than measurements of impervious surface (ISC) and tree canopy cover (TCC) within the stream reach or catchment. Indirect effects of urbanization pressures on avian richness operated through two pathways at multiple spatial scales: reach-scale ISC reduced local TCC, and catchment-scale ISC reduced B-IBI. Therefore, aquatic prey subsidies and riparian habitat conditions can mediate the influence of anthropogenic stressors on avian assemblages. By applying our model to projections of ISC through the year 2100 we show that restoration at multiple spatial scales is necessary to maintain present-day richness levels in the face of continued urban expansion and its effect on aquatic subsidies. These findings indicate that the future conservation of terrestrial and aquatic biodiversity in urban environments is tightly intertwined and dependent on co-management of the landscape.