Whilst the impact of continental and marine nutrient sources on the ecological functioning of coastal food webs is well investigated in temperate regions, tropical ecosystems remain less well understood, in particular coastal lagoons. In this study, the sources of carbon and nitrogen in a coastal lagoon system in the southeast of Madagascar are traced using stable isotopes of carbon (δ13C) and nitrogen (δ15N). Three interconnected coastal lagoons with different degree of river influence and eutrophication are investigated. Their food webs are assessed with respect to spatial and seasonal (wet and dry seasons) variations in lagoon water conditions, as well as with respect to the sources of nutrients and organic matters. Results show that river input is the main source of NO3-, and that NO3- supply is significantly higher during the wet season. In contrast, NH4+ is produced internally in the lagoon, and concentrations are higher during the dry season. A lower δ13C value observed in particulate organic matter (POM; proxy of phytoplankton) indicates terrestrial-riverine carbon inputs, which generally have low δ13C values. During the dry season, exceptionally high δ15N values of lagoon POM suggest the uptake of newly produced lagoon water NH4+ and / or the 15N enrichment of lagoon POM pool due to mineralization, resulting in 15N enrichment in consumers. Moreover, δ13C and δ15N values of consumers (fishes and invertebrates) reflect predominantly those of lagoon POM and sediment organic matter (SOM), suggesting that consumers primarily depend on lagoon POM and SOM as sources of carbon and nitrogen. The δ15N values in consumers further indicate that some species feed on more than one trophic level, suggesting flexible foraging strategy of consumers as a function of food source availability. This study demonstrates the roles of both river inflow and sediment in supplying carbon and nitrogen to a coastal lagoon food web, documenting the ecological implications of seasonal variations in lagoon hydrological conditions.