The Xincun and Li-An lagoons are located on the southeastern coast of Hainan Island, China, and the geomorphology here is characterized by tidal channels/inlets, tidal marshes, coastal dunes and marine terraces. Before the 1980s, these coastal embayments were characterized by a rich biodiversity of coral reefs, seagrass and mangroves. Recently, however, these ecosystems have been extensively interfered by human activities (e. g., agriculture,aquaculture and tourism) and damaged by natural events (e. g. storms and typhoons). These two small tropical sedimentary basins were investigated to understand their sediment infilling and carbon burial patterns in response to tropical extreme storms and anthropogenic processes. Surficial sediment samples and 7 short cores were collected and analyzed to obtain data sets of grain size, organic and inorganic carbon contents, deposition rates, vertical fluxes of sediment and organic carbon. The results obtained show that the lagoons are covered by mud deposits with high organic and inorganic carbon contents. Both organic and inorganic carbon contents in sediments from the Xincun lagoon are higher than those from the Li-An lagoon. The organic carbon burial rate (9*10~6kg/a) in the Xincun lagoon is some 3 times higher than that in the Li-An lagoon (3*10~6kg/a). Provenance analysis indicates that the higher carbon burial in Xincun may have resulted from the larger-area distribution of coral reefs. Likewise, the sharp decline of inorganic carbon contents in Xincun during 1980 ~2000 may be related to dramatic decrease of coral reefs, which suffer greatly from global warming, overfishing and eutrophication. In addition,sediment accumulation and carbon burial of the two lagoons are affected significantly by typhoons. In Xincun, approximately 1.33* 10~7kg/a of sediments were transported to the tidal basin by the typhoon-induced rainfall, which accounts for a third of the total sediment deposition (4.64* 10~7kg/a). Increased typhoon activities may enhance silicate weathering rates and exacerbate sediment loads, thereby increase organic matter and sediment burials in the tidal basins. Hence, the impacts of typhoon on sediment transport and carbon burial need further studies. Furthermore, the organic carbon fluxes from these two lagoons and other embayment along the Hainan Island coastlines demonstrate that tropical coastal embayments make an important contribution to the regional patterns of shallow marine carbon burial. The burial rate of organic carbon of the major (17) embayment on the coast of Hainan Island reaches 0.34 * 10~8 kg/a. The total carbon burial rate would reach an order of magnitude of 10~8 ~ 10~9kg/a. Such a quantity is not small compared with the value (2* 10~9kg/a) for the adjacent continental shelves near Hainan Island.