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Aquatic metabolism is reflected in the dynamics of dissolved oxygen (O₂) and carbon dioxide (CO₂) concentrations. Thus, paired measurements of CO₂ and O₂ concentrations can capture the metabolic characteristics of an ecosystem, with promising results in lakes. Yet, for rivers, hydrological, chemical, and biological processes all influence CO₂ and O₂ concentrations, complicating how paired measurements can be used to infer ecosystem processes. Here we combine a data synthesis with a simple mechanistic model of river metabolism, gas exchange, groundwater inputs and carbonate equilibrium to assess how each imprints upon CO₂ : O₂ patterns. Among the physicochemical processes considered, groundwater inputs substantially influenced CO₂ : O₂ relationships. Regardless, analysis of paired CO₂ : O₂ data resolved predictable differences in ecosystem function across rivers with variable productivity and disturbance, as well as along the river continuum. Results indicate that paired CO₂ : O₂ data can aid in assessments of river metabolism, provided that we account for the dynamic physical environment.