Wetlands rich in carbon are important ecosystems for storing organic carbon, with their carbon storage capacity closely linked to water levels. Therefore, it is valuable to explore the relation between paleohydrological conditions and the organic carbon accumulation in carbon-rich deposits. This study examined the total organic carbon concentration and the molecular and carbon isotope compositions of n-alkanes in Ganhai, a dried up lake located in a region transitioning from a monsoon to an arid climate in north China. The results showed that the apparent carbon accumulation rates (CAR) increased as the East Asian summer monsoon intensified (averaged at 26.5 g C m−2 yr−1, 1 σ = 8.6), but decreased when precipitation levels peaked (averaged at 15.8 g C m−2 yr−1, 1 σ = 2.2). The above relation between precipitation and CAR in Ganhai is supported by the correlation analysis (r = −0.35, p = 0.003). This suggests a threshold relation between wetland carbon accumulation and precipitation in this region. The output of a Bayesian multi-source mixing model, based on the molecular and carbon isotope compositions of long-chain n-alkanes, underscores the significant role of aquatic plants in influencing carbon accumulation in Ganhai during the mid-Holocene, with submersed plants dominating during high CAR periods and floating plants being more prevalent during peak precipitation. The study emphasizes the importance of understanding the hydrological threshold for carbon sequestration and vegetation restoration in carbon-rich wetlands.