In the present study we developed a trophic model (ECOPATH with ECOSIM), to describe the structure and functioning of Bahía Magdalena estuarine ecosystem. The model, constituted by 24 functional groups, indicates that one third of the total ecosystem biomass is produced by secondary and tertiary trophic levels. The magnitude of total flows in the system and the transfer efficiency among trophic levels, are similar to those observed in other tropical systems around the world. A large proportion of the total flows are directed to the maintenance of the trophic web structure. The value of the connectance index (CI) was 0.2, meaning that there is only 20% of realized connections within the web. Benthic primary producers contribute with 53% of the total ascendency. We believe that the energy control in this particular ecosystem is top-down type (through the main predators), suggesting that high-trophic level species negatively affect other groups in the system. This trophic model can be used for exploring different hypothesis concerning the biotic and abiotic mechanisms that modify the structure and functioning of the Bahía Magdalena ecosystem, with the ultimate goal of understanding how this attributes determine the resilience of marine communities.