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Headwater streams are control points for carbon dioxide (CO₂) emissions to the atmosphere, with relative contributions to CO₂emission fluxes from lateral groundwater inputs widely assumed to overwhelm those from in‐stream metabolic processes. We analyzed continuous measurements of stream dissolved CO₂and oxygen (O₂) concentrations during spring and early summer in two Mediterranean headwater streams from which we evaluated the contribution of in‐stream net ecosystem production (NEP) to CO₂emission. The two streams exhibited contrasting hydrological regimes: one was non‐perennial with relatively small groundwater inflows, while the other was perennial and received significant lateral groundwater inputs. The non‐perennial stream exhibited strong inverse coupling between instantaneous and daily CO₂and O₂concentrations, and a strong correlation between aerobic ecosystem respiration (ER) and gross primary production (GPP) despite persistent negative NEP. At the perennial stream, the CO₂–O₂relationship varied largely over time, ER and GPP were uncorrelated, and NEP, which was consistently negative, increased with increasing temperature. Mean NEP contribution to CO₂emission was 51% and 57% at the non‐perennial and perennial stream, respectively. Although these proportions varied with assumptions about metabolic stoichiometry and groundwater CO₂concentration, in‐stream CO₂production consistently and substantially contributed to total atmospheric CO₂flux in both streams. We conclude that in‐stream metabolism can be more important for driving C cycling in some headwater streams than previously assumed.