Riparian and wetland ecosystems (RWEs) are home to many biphasic species, such as amphibians, whose life cycles require both terrestrial and aquatic habitats. This “turquoise infrastructure” has emerged only recently and, because it is complex, little is known to date about how to evaluate its functionality. This paper presents an innovative graph-based model for assessing the connectivity of composite habitats. The model is applied to amphibians at the migration and dispersal ranges in the Essonne department (France). We evaluate the impacts of recent and future (i.e., planned urbanization and drying-up of water bodies due to climate change) landscape transformations on multi-habitat connectivity for these species. Aquatic and terrestrial habitats jointly contribute significantly to the overall habitat connectivity of biphasic species, and changes in landscape configuration can significantly affect composite habitat networks. We find that past land-cover changes had greater negative impacts than those expected from future urbanization. Conversely, the potential future disappearance of ponds because of, for example, climate change could be far more devastating if more than one in four ponds is lost. Turquoise infrastructure supports species with a biphasic lifestyle and makes their multi-habitat networks resilient to urbanization and climate change. In this context, we argue the multi-habitat models can be used relevantly for enhancing and restoring breeding sites, planning, and designing ecological corridors, and/or establishing new protection areas at the landscape scale.