River systems play a pivotal role in transporting and transforming organic carbon (OC) fixed by terrestrial primary production. However, there is a fundamental gap in our understanding of the connectivity of terrestrial, aquatic, and marine carbon budgets due to a lack of measurements along the lower (i.e. tidally-influenced) reaches of large river systems. For example, all estimates of carbon fluxes from the world’s largest river, the Amazon, are based on measurements made at and upstream of Óbidos, roughly 900 km from the mouth. Here we examine the evolution of OC concentrations and composition from Óbidos to two discreet channels near the mouth of the Amazon River during five cruises from 2010 to 2012. OC characteristics of the Tapajós River, which enters the Amazon River downstream of Óbidos, and the Tocantins River, which mixes with the Amazon River plume in the Atlantic Ocean, were also assessed. The average concentration of particulate organic carbon (POC) across the two main channels near the mouth was 0.6 ± 0.3 mg L− 1 during the study period, decreasing from 1.2 ± 1.0 mg L− 1 at Óbidos. Average dissolved organic carbon (DOC) concentrations, on the other hand, increased from 3.9 ± 0.6 mg L− 1 at Óbidos to 4.2 ± 0.9 mg L− 1 across the mouth. The discharge of total OC to the ocean was composed of 89 ± 3% dissolved load, compared to 76 ± 13% at Óbidos. Measurements of bulk OC stable isotopic signatures, chlorophyll a concentrations, and lignin phenol abundance were used to assess unique OC sources along the continuum. For example, the stable isotopic composition of POC and DOC indicated a replacement of highland forest-derived OC with lowland and floodplain-derived OC from Óbidos to the mouth. Likewise, lignin phenol signatures showed an increase in the degradation state of vascular plant-derived OC from Óbidos to the mouth. Results from this study illustrate that the abundance and composition of OC continue to evolve along the lower reaches of large tropical rivers, which has significant implications on estimations of geochemical fluxes to the ocean.