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[Display omitted] • Soil organic carbon and labile organic carbon fractions decreased in the subsidence waterlogging areas. • The largest carbon depletion was observed in the 0–10 cm soil layer. • The liability of particulate organic carbon was highest among the three types of labile organic carbon fractions. • Labile organic carbon fractions were closely correlated with soil properties. • The shallow waterlogging area has the best carbon accumulation potential. The restoration of subsidence waterlogging areas has the potential to facilitate carbon accumulation in coal mining areas with high ground water tables. However, the soil organic carbon (SOC) and labile organic carbon (LOC) have not been sufficiently investigated in different types of subsidence waterlogging areas. In this study, SOC and LOC fractions, including light fraction organic carbon (LFOC), particulate organic carbon (POC), and dissolved organic carbon (DOC) within 0–50 cm soil profiles, were determined in a reference cropland (RC) and three types of subsidence waterlogging area in Xinglongzhuang Coal Mine, Shandong Province, China, including an aquaculture waterlogging area (AWA), deep waterlogging area (DWA) and shallow waterlogging area (SWA) with water depths of 1.8, 3.2, and 0.65 m, respectively. Compared with RC, SOC and LOC decreased by 4.13%, 25.03%, and 77.91% in SWA, DWA, and AWA, respectively. The largest depletion was in the 0–10 cm layer, indicating that there was a time lag for the recovery of the total functional pools of SOC after subsidence. The lability of POC was highest among the three types of LOC fractions, indicating that mining subsidence triggered soil redistribution and impacted on carbon accumulation. With comparatively little soil profile interference in DWA and SWA, the lability of LFOC and POC decreased with soil depth, while the DOC increased. There was a large discrepancy in AWA, with the lability of LOC fractions fluctuating because of soil disturbance by intensive engineering. The LOC fractions were closely associated and correlated with soil properties, especially total nitrogen (TN) and total phosphorus (TP). Restoration and management of the subsidence waterlogging areas have a vital impact on the SOC pool. It was concluded that shallow water and a natural geomorphology-based topography, with little soil disturbance, well-developed vegetation communities, and continuous monitoring of soil and water properties would facilitate the carbon accumulation process. [ABSTRACT FROM AUTHOR]