Dissolved inorganic carbon (DIC) is the most important carbon component in karst aquatic system where fluid is highly transmissive, but has rarely been examined in the subtropical karst critical zone (K‐CZ). In this study, concentrations of dissolved solutes and isotopic compositions of DIC (δ13CDIC) at 11 sites of a 73.4 km2 karstic catchment in Southwestern China were analysed monthly in order to uncover the spatiotemporal variations of both DIC and its dominant sources, and to identify relevant controlling factors. Both DIC concentrations and δ13CDIC were highly variable, ranging from 2.52 to 5.85 mmol l−1 and from −15.7 to −4.5‰, respectively. DIC in underground water (UGW) was higher in concentration and more depleted in 13C compared to surface water (SFS). DIC concentrations showed an inconsistent seasonal trend with other solutes, with higher values in the wet season at some sites. δ13CDIC values were lower in the wet season than in the dry season. The results of mixing model IsoSource revealed spatiotemporal patterns of DIC sources. During the dry season, carbonate weathering was the primary contributor to DIC in UGW (excluding in the middle reaches). However, during the wet season, soil CO2 was the dominant source of DIC in both UGW and SFS, and it was higher than in the dry season. Overall, there are significant spatiotemporal disparities and highly transmissive characteristics of both DIC and its sources in the K‐CZ, which are controlled by multiple factors. This study also highlights that rainfall may play a crucial role in accelerating carbon dynamics in the K‐CZ. High‐frequency sampling campaigns in high‐flow periods and deep analyses are needed in future work to elucidate the related processes and mechanisms. © 2019 John Wiley & Sons, Ltd.