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.