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Abstract. Large-scale lake clusters serve as important freshwater resources in arid and semi-arid regions, but the groundwater recharge patterns sustaining these clusters remain poorly researched. The Songnen Basin, a semi-arid region in northeastern China, contains numerous shallow lakes most of which are not connected to rivers, showing complex interconnections with the groundwater recharge and storage. Here, this paper investigates the role of groundwater in sustaining the freshwater in the lake clusters of the Songnen Basin using remote sensing and isotope analysis, especially during the winter of Chagan Lake, the largest lake in this basin. Our results suggest that deep groundwater upwelling through fault zones is a significant recharge source for Chagan Lake, contributing to the frequent occurrence of stable ice-free areas. Isotopic tracers indicate that this deep groundwater does not originate from local precipitation but likely originates from external sources, potentially the Tibetan Plateau. A deep-circulation groundwater pattern is proposed, suggesting that water-conduiting channels exist under the deep lithosphere in arid and semi-arid regions. When these channels are destroyed by earthquakes, deep-circulating groundwater would rises through faults and recharges lake clusters.