Widespread cold seeps along continental margins are significant sources of dissolved carbon to the ocean water. However, little is known about the methane turnovers and possible impact of seepage on the bottom seawater at the cold seeps in the South China Sea (SCS). We present seafloor observation and porewater data of six push cores, one piston core and three boreholes as well as fifteen bottom-water samples collected from four cold seep areas in the northwestern SCS. The depths of the sulfate–methane transition zone (SMTZ) are generally shallow, ranging from ~7 to <0.5 mbsf (meters below seafloor). Reaction-transport modelling results show that methane dynamics were highly variable due to the transport and dissolution of ascending gas. Dissolved methane is predominantly consumed by anaerobic oxidation of methane (AOM) at the SMTZ and trapped by gas hydrate formation below it, with depth-integrated AOM rates ranging from 59.0 and 591 mmol m⁻² yr⁻¹. The δ¹³C and Δ¹⁴C values of bottom-water dissolved inorganic carbon (DIC) suggest discharge of ¹³C- and ¹⁴C-depleted fossil carbon to the bottom water at the cold seep areas. Based on a two-endmember estimate, cold seeps fluids likely contribute 16–26% of the bottom seawater DIC and may have an impact on the long-term deep-sea carbon cycle. Our results reveal the methane-related carbon inventories are highly heterogeneous in the cold seep systems, which are probably dependent on the distances of the sampling sites to the seepage center. To our knowledge, this is the first quantitative study on the contribution of cold seep fluids to the bottom-water carbon reservoir of the SCS, and might help to understand the dynamics and the environmental impact of hydrocarbon seep in the SCS.