We report on the water column biogeochemistry in adjacent mangrove and seagrass systems in Gazi Bay (Kenya), with a focus on assessing the sources and cycling of organic and inorganic carbon. Mangrove and seagrass-derived material was found to be the dominant organic carbon sources in the water column, and could be distinguished on the basis of their δ 13C signatures and particulate organic carbon:total suspended matter (POC/TSM) ratios. Spatially, a distinct boundary existed whereby the dominance of mangrove-derived material decreased sharply close to the interface between the mangrove forest and the dense seagrass beds. The latter is consistent with the reported export of mangrove-derived material, which is efficiently trapped in the adjacent seagrass beds. There were significant net inputs of POC and dissolved organic carbon (DOC) along the Kidogoweni salinity gradient, for which the δ 13CPOC signatures were consistent with those of mangroves. DOC was the dominant form of organic carbon in both mangrove and seagrass beds, with DOC/POC ratios typically between 3 and 15. Dynamics of dissolved inorganic carbon in the creeks were strongly influenced by diagenetic C degradation in the intertidal mangrove areas, resulting in significant CO2 emission from the water column to the atmosphere. Although highest partial pressure of CO2 (pCO2) values and areal CO2 flux rates were observed in the mangrove creeks, and the water column above the seagrass beds was in some locations a net sink of CO2, most of the ecosystems' emission of CO2 to the atmosphere occurred in the seagrass beds adjacent to the mangrove forest. The presence of dense seagrass beds thus had a strong effect on the aquatic biogeochemistry, and resulted in trapping and further mineralization of mangrove-derived POC, intense O2 production and CO2 uptake. The adjacent seagrass beds provide a large area with conditions favorable to exchange of CO2 with the atmosphere, thereby limiting export of mangrove-derived organic and inorganic carbon toward the coastal ocean.