Recent studies have remarked on the importance of direct CO2 release from river water into the atmosphere on the global carbon cycle over a short timescale. In this study, we investigated carbonate systems, including spatial and seasonal variations of pCO2, in three major Himalayan rivers in Bangladesh: the Ganges, Brahmaputra, and Meghna Rivers, and their potential importance. Although pCO2 is known to be low in the upper reaches of these rivers, owing to active chemical weathering, we observed pCO2 values higher than the atmospheric pCO2 level along their lower reaches, where deep soils have developed and where high air temperatures promote active soil respiration. By a simple mixing calculation, we found that seasonal variations in these river water carbonate systems are controlled by subsurface water flows. In the rainy season, most of the lowlands are inundated, and the contribution of subsurface flow to river water carbonate systems increases, resulting in higher pCO2 values. In future research, more detailed spatial and seasonal investigations are required to clarify the role of terrestrial ecosystems, including rivers and the CO2 flux to the atmosphere, in the global carbon cycle and to examine how that role will change under global warming.