Urban blue and green spaces, like ponds and parks, can mitigate the negative effects of urbanization on biodiversity by providing diverse, connected habitats and enabling resource flows between ecosystems. While studies have evaluated these spaces for terrestrial and aquatic communities individually, few have examined shared factors influencing both communities simultaneously. Consequently, it is unclear how these spaces should be conceived and maintained to support the diversity of both aquatic and terrestrial species, as well as their interactions. Here, we use environmental DNA (eDNA) metabarcoding to identify shared drivers and assess if and how aquatic and terrestrial invertebrate communities are coupled across 54 paired aquatic and terrestrial habitats along an urbanization gradient in the city of Zurich, Switzerland. Contrary to general expectations, we find no significant correlation in aquatic and terrestrial community structure, which we attribute to distinct drivers identified for both communities. Aquatic communities were primarily influenced by local factors related to habitat quality, while terrestrial communities were associated to landscape drivers pertaining to habitat quantity, suggesting that different processes at different spatial scales need to be considered to support both communities. Furthermore, with increasing urbanization, aquatic and terrestrial communities exhibited signs of decoupling driven by the filtering of organisms straddling ecosystem boundaries. We conclude that increasing levels of urbanization weaken resource flow between aquatic and terrestrial environments. By employing eDNA across ecosystem boundaries, our study highlights the critical importance of both the quality and quantity of urban habitats in conserving aquatic and terrestrial communities, as well as their linkages.