To better understand the depositional constraints on the fingerprint characteristics of methane isotopes, we present a set of carbon/hydrogen isotopic data for CH4, CO2, pore water, carbonate, and total organic carbon along a 70‐m sedimentary core. The sedimentary facies (Units I, II, and III from upper to bottom) suggested depositional environments of the present estuary, shallow marine, and floodplain‐estuary. Calculations suggested that around 86% of methane was produced through the CO2 reduction pathway. In this pathway, the hydrogen in CH4 is from ambient water, while the carbon is from dissolved inorganic carbon. Correspondingly, our study showed that the values of δDCH4 displayed similar trends with those of δDH2O and Cl− concentrations along the depth profiles. The low δDCH4 below 44.5 m corresponded to low δDH2O and low salinity during the cold and low‐sea‐level period. The values of δ13CCH4 generally synchronously changed with those of δ13CCO2. The variation trends of δ13CCH4 and δ13CCO2 were the same with δ13Ccarbonate from 10 to 70 m depth but decoupled above 10 m. The values of δ13CCH4 in Units II and III were correlated with the δ13Ccarbonates, which is related to the sedimentary processes. But decoupling of low values of δ13CCH4 and δ13CCO2 from δ13Ccarbonates in Unit I may be related to preferential microbial consumption of labile compounds with light carbon isotopic compositions, such as lipids. In short, the variations of δ13CCH4 and δDCH4 were largely related to the sedimentary process, which controlled the isotopic compositions of both water and carbonate.