<p>Under rapid urbanization, waterfront space is increasingly encroached upon, disconnecting water cultural heritage protection from ecosystem restoration and undermining urban resilience. Focusing on the J section of the Beijing–Hangzhou Grand Canal, this paper proposes a “culture–ecology” framework to integrate an ecological–cultural security pattern. Five factors—water retention, soil conservation, biodiversity, water environmental capacity and water culture conservation—are coupled to establish a priority evaluation system for ecological protection. Based on patch connectivity and patch size, ecological sources are screened. Four resistance indicators—elevation, slope, land use and distance to water—are used to build ecological and heritage corridor resistance surfaces. Employing circuit theory and the minimum cumulative resistance model, point and linear elements are identified, and “point–line–area” components are integrated into an overall ecological security pattern. Results show that high-priority conservation areas occupy 11.48% of the region and coincide spatially with key water systems and cultural heritage sites, confirming alignment between hydrological heritage and ecosystems. Eight ecological sources are identified; the largest and most connected lie at the confluence of the Grand Canal and the Yangtze River and along the old Tongyang Canal. Twelve ecological corridors, one hundred heritage corridors, seventeen pinch points and twenty-four barriers are mapped and ranked. An integrated structure of “one axis, two corridors, two belts, three cores and five zones” is proposed, accompanied by differentiated restoration and recreational strategies, offering an operational spatial framework for sustainable “culture–ecology” development in rapidly urbanizing regions.</p>