The coupled carbonate weathering represents a significant carbon sink and can be controlled by the riverine hydrochemical variations. However, magnitudes, variations, and mechanisms responsible for the carbon sink produced by coupled carbonate weathering are unclear. In view of this, temperature, pH, dissolved oxygen, turbidity, electrical conductivity, and discharge of the Xijiang River at Wuzhou Hydrologic Gauging Station was recorded during October 2013 to September 2015 to elucidate the temporal variations in riverine hydrochemistry and their controlling mechanisms. To obtain the complete carbon sink flux (CSF) produced by coupled carbonate weathering with terrestrial aquatic photosynthesis in the river basin, the fluxes of dissolved inorganic carbon (DIC), autochthonous organic carbon (AOC, sourced from the transformation of DIC via aquatic photosynthesis), and sedimentary AOC were all considered. The results show that seasonal hydrochemical variations in the Xijiang River were related not only to dilution effects but also aquatic primary production. These results demonstrate that the variations in discharge caused by rainfall played a dominant role in controlling the variations in the CSF due to the chemostatic behavior of DIC and dissolved organic carbon (DOC). The CSF of the Xijiang River produced by coupled carbonate weathering was calculated as 11.06 t C km a, including DIC carbon sink flux of 6.56 t C km a, AOC flux (F) of 2.25 t C km a, and sedimentary AOC flux (F) of 2.25 t C km a. The F and F together accounted for approximately 69% of DIC carbon sink flux, or approximately 41% of the CSF, indicating that the riverine AOC flux may be high and must be considered in the estimation of rock weathering-related carbon sinks.