Abstract Evaluating multiple competing biotic and abiotic processes and how they interact with carbon dioxide (CO2) in aquatic systems, is critical to understanding regional and global carbon cycles. Here, we used an aquatic continuum of the Bahe watershed, within a semi‐arid region, to establish a comprehensive conceptual framework for identifying CO2 drivers from measured hydrochemical properties, heavy metals (HMs), dissolved organic matter (DOM) characteristics, and phytoplankton properties. The results revealed that dissolved CO2 (cCO2) showed large spatiotemporal variability. Our results highlight that carbonate buffering coupled with aquatic photosynthesis, collectively regulated the CO2 dynamics. Additionally, DOM and HMs have biogeochemical pathways that are common to CO2 dynamics (i.e., the biological carbon pump). In particular, HMs were found to have a high potential for signaling CO2 dynamics. The findings contribute to a better understanding of the carbon dynamics in an aquatic continuum in a semi‐arid region, together with the underlying mechanisms.