Suitability networks for restoration: Hydrobiogeochemical flows imprinting habitat-forming species

Coastal habitats, such as oyster reefs, are critical land–sea ecotones that support biodiversity, ecosystem services, and ecosystem resilience. However, restoration of oyster reefs in river deltas and other coastal ecosystems remains challenged by the lack of scalable tools capable of quantifying how environmental heterogeneity shapes connectivity and reef structure across fragmented ecotones. Here, we introduce a generalizable Topologic Systemic Ecograph (TIE) model that integrates three-dimensional hydrodynamic and biogeochemical fields with habitat occurrence data to infer ecological flows, flow-defined connectivity, and basins derived from predicted habitat suitability. By adapting hydro-inspired flow-routing algorithms and network-theoretic analysis, we construct the Oyster Flow Graph (OFG) and delineate Oyster Connectivity Basins (OCBs)— ecograph and ecosheds —providing spatially explicit ecological patterns, including eco-environmental feedbacks that support biogenic structures across ecosystem scales. Application of the TIE framework to biogenic structures such as oyster reefs in the Pearl River Delta, Greater Bay Area, reveals pronounced regional differentiation, with central delta basins functioning as connectivity hubs and peripheral basins acting as flow bottlenecks. Stable, high-suitability zones emerge along sheltered deltaic and estuarine habitats, indicating conditions favorable for reef establishment and persistence. The inferred ecological flow topology is physically consistent with regional hydrodynamic patterns for 66.34% of flow directions, and Random Forest modeling highlights key hydro-biogeochemical drivers shaping network connectivity. At the delta scale, nitrate concentration, latitudinal (North–South) and vertical velocities at intermediate and deep depths, as well as chlorophyll-a, emerge as the predominant factors. Under high-flow conditions, vertical and longitudinal/cross-delta (East–West) velocities become the most important features. These flow interactions reflect the predominance of deltaic hydrology in governing nutrient transport and residence within reef habitats, thereby influencing reef morphology, ecological fitness, and cascading ecosystem services. Temperature and salinity emerge as second-order factors, given their relatively weak interactions with other environmental variables in defining ecological flows. Overall, the proposed TIE model and framework advance precision restoration design by explicitly linking inferred eco-environmental flows derived from habitat suitability to ecological connectivity expressed as topology, and are transferable to other coastal and marine habitats where eco-environmental pressures can be structured to trigger ecological self-emergence. • A novel Topological Systemic Ecograph (TIE) model infer the flows, connectivity and basins of oyster reefs. • Flow corridors are extracted from 3D environmental gradients using network-based models. • In River Deltas, Central basins serve as connectivity hubs while cross-delta basins are dispersal bottlenecks, where connectivity is shaped by hydrologic flows. • Key drivers of connectivity include nitrate levels and mid-layer horizontal flow velocity. • TIE enables targeted, scalable oyster reef restoration across dynamical coastal ecosystems.