The carbon isotopic composition (δ13C) of dissolved and particulate inorganic carbon (DIC; PIC) was used to compare and analyze the origin, dynamics and evolution of inorganic carbon in two headwater tributaries of the Xi River, Southwest China. Carbonate dissolution and soil CO2 were regarded as the primary sources of DIC on the basis of δ13CDIC values which varied along the Nanpan and Beipan Rivers, from −13.9‰ to 8.1‰. Spatial trends in DIC differed between the two rivers (i.e., the tributaries), in part because factors controlling pCO2, which strongly affected carbonate dissolution, differed between the two river basins. Transport of soil CO2 and organic carbon through hydrologic conduits predominately controlled the levels of pCO2 in the Nanpan River. However, pCO2 along the upper reaches of the Nanpan River also was controlled by the extent of urbanization and industrialization relative to agriculture. DIC concentrations in the highly urbanized upper reaches of the Nanpan River were typical higher than in other carbonate-dominated areas of the upper Xi River. Within the Beipan River, the oxidation of organic carbon is the primary process that maintains pCO2 levels. The pCO2 within the Beipan River was more affected by sulfuric acid from coal industries, inputs from a scenic spot, and groundwater than along the Nanpan River. With regards to PIC, the contents and δ13C values in the Nanpan River were generally lower than those in the Beipan River, indicating that chemical and physical weathering contributes more marine carbonate detritus to the PIC along the Beipan River. The CO2 evasion flux from the Nanpan River was higher than that in the Beipan River, and generally higher than along the middle and lower reaches of the Xi River, demonstrating that the Nanpan River is an important net source of atmospheric CO2 in Southwest China.