Urban–rural fringes (URFs) are crucial for biodiversity yet often neglected in conservation efforts. This study refines URF habitat evaluation and integrates it into a coordinated ecological network (EN) and territorial planning framework. Using Qingpu District, Shanghai as a case study, we defined its URF via k-means clustering of night-time light data and applied the InVEST model, MSPA, Integrated Habitat Value, Patch Importance, and Betweenness Centrality analyses to identify high-value URF habitats. Furthermore, we constructed the EN using circuit theory and evaluated the impact of URF sources on network connectivity and construction costs. Our findings reveal that integrating URF sources increased connectivity indices significantly (α by 127.18%, β by 47.00%, and γ by 33.4%) and decreased construction costs (CR index by 0.07). Despite these benefits, under China’s “Three Zones and Three Lines” policy, 78.18% of Qingpu’s URF sources remain unprotected, with 56.78% at risk of conversion to construction land. Our study proposes a comprehensive evaluation system for URF habitats and strategic recommendations for their incorporation into regional ENs, thus informing policy making and planning for more inclusive ecological conservation.

Freshwater ecosystems—home to roughly 10% of known species—are losing biodiversity to river-morphology alteration, hydraulic infrastructure, and pollution, yet most ecological network (EN) studies focus on terrestrial systems and overlook hydrological connectivity under human disturbance. To address this, we devised and tested a dual EN framework in the Yangtze River Delta’s Ecological Green Integration Demonstration Zone, constructing freshwater and terrestrial networks independently before merging them. Using InVEST Habitat Quality, MSPA, the MCR model, and Linkage Mapper, we delineated sources and corridors: freshwater sources combined NDWI-InVEST indicators with a modified, sluice-weighted resistance surface, producing 78 patches (mean 348.7 ha) clustered around major lakes and 456.4 km of corridors (42.50% primary). Terrestrial sources used NDVI-InVEST with a conventional resistance surface, yielding 100 smaller patches (mean 121.6 ha) dispersed across woodlands and agricultural belts and 658.8 km of corridors (36.45% primary). Unified models typically favor large sources from dominant ecosystems while overlooking small, high-value patches in non-dominant systems, generating corridors that span both freshwater and terrestrial habitats and mismatch species migration patterns. Our dual framework better reflects species migration characteristics, accurately captures dispersal paths, and successfully integrates key agroforestry-complex patches that unified models miss, providing a practical tool for biodiversity protection in disturbed freshwater–terrestrial landscapes.