Rivers are important sites for carbon (C) transport and critical components of the global C cycle that is currently not well constrained. However, little is known about C species’ longitudinal and temporal changes in large tropical rivers. The Usumacinta River is Mexico’s main lotic system and the tenth largest in North America. Being a tropical river, it has a strong climatic seasonality. This study aims to evaluate how organic (DOC and POC) and inorganic (DIC and PIC) carbon change spatially and seasonally along the Usumacinta River (medium and lower basin) in rainy (RS-2017) and dry (DS-2018) seasons and to estimate C fluxes into the southern Gulf of Mexico. Concentrations of DOC, POC, DIC, and PIC ranged from 0.88 to 7.11 mg L−1, 0.21 to 3.78 mg L−1, 15.59 to 48.27 mg L−1, and 0.05 to 1.51 mg L−1, respectively. DOC was the dominant organic species (DOC/POC > 1). It was ~doubled in RS and showed a longitudinal increase, probably through exchange with wetlands and floodplains. Particulate carbon showed a positive relationship with the total suspended solids, suggesting that in RS, it derived from surface erosion and runoff in the watershed. DIC is reported for the first time as the highest concentration measured in tropical rivers in America. It was higher in the dry season without a longitudinal trend. The C mass inflow–outflow balance in the RS suggested net retention (DOC and POC sink) in floodplains. In contrast, in the DS, the balance suggested that floodplains supply (C source) autochthonous DOC and POC. The lower Usumacinta River basin is a sink for DIC in both seasons. Finally, the estimated annual C export for the Usumacinta-Grijalva River was 2.88 (2.65 to 3.14) Tg yr−1, of which DIC was the largest transported fraction (85%), followed by DOC (10%), POC (4%), and PIC (<1%). This investigation is the first to present the C loads in a Mexican river.