Multiple processes support the significant efflux of carbon dioxide (CO₂) from rivers and streams. Attribution of CO₂ oversaturation will lead to better quantification of the freshwater carbon cycle and provide insights into the net cycling of nutrients and pollutants. CO₂ production is closely related to O₂ consumption because of the metabolic linkage of these gases. However, this relationship can be weakened due to dissolved inorganic carbon inputs from groundwater, carbonate buffering, calcification, and anaerobic metabolism. CO₂ and O₂ concentrations and other water quality parameters were analyzed in two data sets: a synoptic field study and nationwide water quality monitoring data. CO₂ and O₂ concentrations were strongly negatively correlated in both data sets (ρ = −0.67 and ρ = −0.63, respectively), although the correlations were weaker in high‐alkalinity environments. In nearly all samples, the molar oversaturation of CO₂ was a larger magnitude than molar O₂ undersaturation. We used a dynamically coupled O₂CO₂ model to show that lags in CO₂ air‐water equilibration are a likely cause of this phenomenon. Lags in CO₂ equilibration also impart landscape‐scale differences in the behavior of CO₂ between high‐ and low‐alkalinity watersheds. Although the concept of carbonate buffering and how it creates lags in CO₂ equilibration with the atmosphere is well understood, it has not been sufficiently integrated into our understanding of CO₂ dynamics in freshwaters. We argue that the consideration of carbonate equilibria and its effects on CO₂ dynamics are primary steps in understanding the sources and magnitude of CO₂ oversaturation in rivers and streams.