Global urbanization is driving a rising demand for sand and gravel, which has intensified riverbed mining. This threatens fluvial stability, flood safety, and ecological integrity. Although previous studies have documented localized geomorphic and hydrological impacts, systematic assessments that integrate long-term incision trends, embankment stability mechanisms, and resource optimization under multiple objectives remain limited. In this study, we investigate the Wengang section of the Fu River (Jiangxi, China), a sediment-deficient river reach subjected to decades of intensive mining. Through the application of hydrosediment analysis, hydrodynamic modeling, geotechnical–hydrological–mechanical (GHM) simulations, and a dynamic optimization model, the sustained impacts of mining are quantified, and science-based management strategies are proposed. The results indicate that extensive excavation has resulted in irreversible riverbed incision, with a net volume increase of 12.97 × 10⁶ m³ between 2003 and 2023, far exceeding the natural sediment deposition volume (0.853 × 10⁶ m³). Although the overall longitudinal profile remains stable, localized flow velocities in the primary mining area are increased by 0.22–0.39 m/s. A GHM analysis identifies a critical safe distance of 13–14 m between pit edge and embankment toe and demonstrates that wide-shallow pit morphology is associated with reduced stability risk compared to narrow-deep pits. Based on these constraints, an economic optimization model incorporating flood safety and market demand is developed, yielding an optimal extraction plan for 2024–2028 with a total volume of 4.4848 million tons and an estimated revenue of 50.03 million USD. This study provides an integrated framework for assessing mining impacts and offers actionable strategies to support sustainable sediment management in vulnerable river systems.