High-frequency, paired measurements of the partial pressure of CO₂ (pCO₂) and dissolved O₂ were combined with dissolved organic matter (DOM) characterization to investigate diurnal (7:00–19:00) and seasonal variations in CO₂ dynamics in the lower Ganges River. Diurnal variations in pCO₂ shifted seasonally, concurring with changes in DOM optical properties, biodegradable DOM, and O₂ departures from atmospheric equilibrium (ΔO₂). Increased pCO₂ and CO₂ flux (FCO₂) in August–September corresponded to monsoonal floods carrying more terrestrial materials. Lower dry-season pCO₂ and FCO₂ concurred with higher ΔO₂, and exhibited strong relationships with DO and pH, indicating a dominant influence of phytoplankton production. Despite large variations in pCO₂, the year-long positive FCO₂ implied that the lower Ganges acted as a CO₂ source, reaching 122 mmol m⁻² d⁻¹. Increasing hydrologic variability and pollution in the Ganges Basin can amplify pCO₂ variations linked to seasonal shifts in terrestrial inputs and phytoplankton production.