Intensive extraction in shallow coal seam groups poses a severe threat to regional hydrogeological stability. This study investigates the evolutionary laws of water-conducting fracture zone (WCFZ) height and phreatic level response at the Wanli No. 1 Mine. Although limited to a two-dimensional physical model and a single-case study, the research integrates field monitoring with similarity simulations to evaluate the efficacy of gangue grouting backfilling (GGB). The results reveal a significant superposition effect in dual-seam mining, where cumulative disturbances trigger the reactivation of upper-seam fractures, causing the WCFZ to penetrate the surface (170 m)—a phenomenon absent in single-seam mining. Scientifically, this work identifies a dual-threshold effect for ecological and structural preservation. While an equivalent filling rate (η) of 35% is sufficient to maintain the ecological water level in single-seam mining, dual-seam extraction requires a minimum η of 65% to restrict phreatic drawdown within the 1.5 m ecological threshold. Notably, while the laboratory model suggests a higher mechanical safety limit of η = 80% to prevent fracture propagation, the 65% threshold provides a balance between backfilling efficiency and environmental protection. The primary scientific contribution of this study is the quantification of the coupling relationship between overburden mechanical stability and long-term ecological functions. By shifting the overburden failure mode from “surface-penetrating fracturing” to “controlled bending subsidence,” this research provides a robust theoretical foundation for decoupling mining intensity from hydrogeological degradation in fragile multi-seam environments.