In the global carbon cycle, rivers are the main transport channel for terrestrial carbon sources into the ocean, and their CO2 fluxes at the water–air interface affect the carbon budget. As an important component of the carbon cycle in the terrestrial ecosystem, karst regions exhibit carbon source and sink effects due to their special environmental conditions. To elaborate the spatial and temporal distribution of CO2 fluxes at the water–air interface of karst rivers and the influencing factors, systematic monitoring of small karst rivers in southwest China was conducted between November and December 2019 and between June and July 2020, respectively. The results show that: (1) the water chemistry of Chiwuxi River belonged to the HCO3–Ca–Mg type, and Ca2+ and HCO3− temporally showed a larger concentration in the dry season than in the wet season. (2) CO2 partial pressure (pCO2) and CO2 fluxes showed a seasonal characteristic of higher values in the wet season than in the dry season. pCO2 ranged from 323.59 to 1380.38 μatm and CO2 fluxes ranged from −24.31 to 353.74 mmol (m2 d)−1. During the wet season, the Chiwuxi River showed a carbon source effect. During the dry season, the photosynthesis of aquatic plants reduced CO2 outgassing. (3) Isotopic compositions of dissolved inorganic carbon (δ13CDIC) showed a higher value in the dry season than in the wet season. The dissolved inorganic carbon mainly originated from soil CO2 and carbonate weathering. To improve the understanding of riverine carbon cycling, it is necessary to study CO2 fluxes at the water–air interface of small rivers in the karst region. Thus, this will help to reduce the uncertainty of CO2 fluxes in global rivers.