Marginal sea biogeochemical cycles are either dominated by continental processes, or oceanic processes where deep marginal-sea basins are effectively influenced by the global ocean deep water. However, how those different processes influence the global carbon cycles under different hydrological settings are not fully understood. By studying the sedimentary calcium carbonate (CaCO3) distributions in several Western-Pacific (WP) marginal seas, we theoretically explain how their distribution features are shaped by different conditions. Our results suggest that, among all sedimentary CaCO3 data only records from the Tasman Sea present similar patterns with those from the global ocean, reflecting remarkable ocean dominated features in carbonate chemistry. While in other basins, carbonate distributions show different characteristics mostly associated with their unique hydrological settings and ecosystem features. Therefore, future interpretation of marginal-sea CaCO3 data in terms of global carbon cycles and large-scale climate changes should be treated with particular cautions.