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Abstract The permafrost active layer is a key supplier of soil organic carbon and mineral nutrients to Arctic rivers. In the active layer, sites of soil-water exchange are locations for organic carbon and nutrient mobilization. Previously these sites were considered as connected during summer months and isolated during winter months. Whether soil pore waters in active layer soils are connected during shoulder seasons is poorly understood. In this study, exceptionally heavy silicon isotope compositions in soil pore waters show that during late winter, there is no connection between isolated pockets of soil pore water in soils with a shallow active layer. However, lighter silicon isotope compositions in soil pore waters reveal that soils are biogeochemically connected for longer than previously considered in soils with a deeper active layer. We show that an additional 21% of the 0–1 m soil organic carbon stock is exposed to soil - water exchange. This marks a hot moment during a dormant season, and an engine for organic carbon transport from active layer soils. Our findings mark the starting point to locate earlier pathways for biogeochemical connectivity, which need to be urgently monitored to quantify the seasonal flux of organic carbon released from permafrost soils.