As an important component of inland water, the primary factors affecting the carbon cycle in karst river–lake systems require further investigation. In particular, the impacts of climatic factors and the biological carbon pump (BCP) on carbon dioxide (CO₂) exchange fluxes in karst rivers and lakes deserve considerable attention. Using quarterly sampling, field monitoring, and meteorological data collection, the spatiotemporal characteristics of CO₂ exchange fluxes in Erhai Lake (a typical karst lake in Yunnan, SW China) and its inflow rivers were investigated and the primary influencing factors were analyzed. The average river CO₂ exchange flux reached 346.80 mg m⁻² h⁻¹, compared to −6.93 mg m⁻² h⁻¹ for the lake. The carbon cycle in rivers was strongly influenced by land use within the basin; cultivated and construction land were the main contributors to organic carbon (OC) in the river (r = 0.66, p < 0.01) and the mineralization of OC was a major factor in CO₂ oversaturation in most rivers (r = 0.76, p < 0.01). In addition, the BCP effect of aquatic plants and the high pH in karst river–lake systems enhance the ability of water body to absorb CO₂, resulting in undersaturated CO₂ levels in the lake. Notably, under rainfall regulation, riverine OC and dissolved inorganic carbon (DIC) flux inputs controlled the level of CO₂ exchange fluxes in the lake (r_OC = 0.78, p < 0.05; r_DIC = 0.97, p < 0.01). We speculate that under future climate and human activity scenarios, the DIC and OC input from rivers may alleviate the CO₂ limitation of BCP effects in karst eutrophication lakes, possibly enabling aquatic plants to convert more CO₂ into OC for burial. The results of this research can help advance our understanding of CO₂ emissions and absorption mechanisms in karst river–lake systems.