Despite carbon (C) exports from continents being crucial in the connection between terrestrial, atmospheric, and oceanic C, there is still limited understanding of the dynamics of C within river basins. The objective of this work was to assess the changes in particulate (POC) and dissolved organic (DOC) and inorganic C (PIC: particulate inorganic carbon, DIC: dissolved inorganic carbon) content, quality, and fluxes within a river basin from its headwaters to its exit at the ocean. A survey was designed in the Thukela basin (from 2012 to 2013 and at six nested catchments ranging from ~10 to ~30,000 km2) in the east of South Africa to evaluate the content, fluxes, and quality (UV spectral slope, 13C, CO2 effluxes from runoff) of the transported C in conjunction with chemical elements (Si, Na) for discriminating between the water sources and estimating C dynamics during low flows. Total carbon exports decreased continuously from 9.75 km2 in the headwater (31.9 kg C km−2 y−1) to ocean (4.7 kg C km−2 y−1) with the highest decrease occurring between the catchment (7614 km2) and large catchment (14,478 km2). About 80% of C exports from the headwaters were POC, followed by DIC (10%) and DOC (10%), while at the ocean, the proportions were 31% (POC), 45% (DIC), 23% (DOC), and 0.7% (PIC). Moreover, there was a sharp decrease in the dissolved organic matter aromaticity from the headwater to ocean and for both DOC and POC that did not correspond to changes in water sources along the river (as indicated by a relatively constant Si/Na ratio). This pointed to the decomposition in the river of the dissolved organic matter originating from soils and to the within-stream organic production. Further in situ investigations need to be performed to quantify the within-stream inputs.