Mitigating shoreline erosion is a key issue in coastal management that lies at the intersection of science, engineering and policy. It involves multiple stakeholders that often prevents the sustainable development of coastal communities in response to a changing climate. Pingtan Island in Fujian Province, China represents a prominent example of the challenges coastal managers face in balancing nature-based solutions with increasing tourism and economic growth. As a result, the island is experiencing a number of environmental challenges. Compounded with storm impacts caused by typhoons and strong prevailing winds, the island is undergoing widespread coastal erosion. Here, we focus on geomorphic responses of five representative beach-dune systems through the lens of geophysics that are subject to various stages of coastal modification. We acquired a suite of multi-frequency ground penetrating radar surveys to image subsurface structures at different depths and spatial resolution. This approach enabled us to compare beach-dune stratigraphy shaped by natural morphodynamics with human-modified perturbations caused by artificial dune construction, sand fence installation, artificial planting, and beach nourishment. Results from the largest and most-visited beach in Changjiang’Ao are unlike typical GPR radargrams reported in the literature. This beach has undergone protection measures to reduce coastal erosion combining clay layer pavement over the dune system to encourage tree growth and sand fence installation to promote the development of artificial dunes. The clay layer and disturbance from sand fences is evident in the radargrams and does not resemble typical foreslope, rearslope, and dune core stratigraphy. Despite large-scale dune restoration, the dune system is characterized by blowouts and is transgressing inland. Overall, the stratigraphic structures are different compared to the beach-dune system at Tannan Bay, that are more typical of a “natural” coast. The absence of the clay layer and artificial tree planting in Tannan Bay enables pioneer species to more effectively stabilize the dune system and has important implications for future restoration activities in Chanjiang’Ao. By integrating high-resolution geophysical data with coastal governance, our project will provide critical decision support for ecological security within the framework of Pingtan’s "International Tourism Island" construction. Ultimately, this approach transforms scientific discovery into actionable policy tools, fostering a synergistic balance between regional economic growth and the long-term preservation of island ecosystems. This analysis will offer recommendations on how artificial interventions, such as clay layers, influence coastal processes, thereby providing scientific references for future nature-based restoration and sustainable coastal protection.