Madagascar’s largest estuary (Betsiboka) was sampled along the salinity gradient during the dry season to document the distribution and sources of particulate and dissolved organic carbon (POC, DOC) as well as dissolved inorganic carbon (DIC). The Betsiboka was characterized by a relatively high suspended matter load, and in line with this, low DOC/POC ratios (~0.4–2.5). The partial pressure of CO2 (pCO2) was generally above atmospheric equilibrium (270–1530 ppm), but relatively low in comparison to other tropical and subtropical estuaries, resulting in low average CO2 emission to the atmosphere (9.1 ± 14.2 mmol m-2 d-1). Despite the fact that C4 vegetation is reported to cover >80% of the catchment area, stable isotope data on DOC and POC suggest that C4 derived material comprises only ~30% of both pools in the freshwater zone, increasing to ~60–70% and 50–60%, respectively, in the oligohaline zone due to additional lateral inputs. Sediments from intertidal mangroves in the estuary showed low organic carbon concentrations (<1%) and d13C values (average -19.8‰) consistent with important inputs of riverine imported C4 material. This contribution was reflected in d13C signatures of bacterial phospholipid derived fatty acids (i + a15:0), suggesting the potential importance of terrestrial organic matter sources for mineralization and secondary production in coastal ecosystems.
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