This study investigates groundwater flow reversal and fault-induced aquifer segmentation in the Zazari–Cheimaditida lake system of Northern Greece, a tectonically active basin impacted by extensive lignite mining. Using long-term piezometric data, elevation measurements, and hydrogeological cross-sections, we assess flow regimes, drawdown patterns, and the hydraulic role of fault structures. A major cone of depression (>40 m) has formed around the Amyntaio Lignite Mine, reversing regional groundwater flow toward the excavation void. Fault zones function either as barriers or conduits, as quantified through a newly proposed Tectonic Influence Index (TII). Results reveal a dual aquifer system: a shallow, seasonally artesian phreatic aquifer connected to Lake Zazari, and a deeper, confined aquifer hydraulically decoupled from surface waters. These findings highlight the strong influence of structural segmentation on groundwater dynamics in post-mining environments. The study proposes a conceptual hydrostructural model to guide adaptive groundwater management in fault-controlled basins. The framework supports efforts to maintain aquifer sustainability during the transition from lignite-based energy, especially under evolving climate and land-use conditions. The approach presented here is transferable to other tectonically segmented mining basins undergoing ecological and policy-driven restoration.