Stream metabolism sources a large fraction of carbon dioxide to the atmosphere in two hydrologically contrasting headwater streams.

Headwater streams are control points for carbon dioxide (CO2) emissions to the atmosphere, with relative contributions to CO2 emission fluxes from lateral groundwater inputs widely assumed to overwhelm those from in‐stream metabolic processes. We analyzed continuous measurements of stream dissolved CO2 and 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 CO2 emission. 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 CO2 and O2 concentrations, and a strong correlation between aerobic ecosystem respiration (ER) and gross primary production (GPP) despite persistent negative NEP. At the perennial stream, the CO2–O2 relationship varied largely over time, ER and GPP were uncorrelated, and NEP, which was consistently negative, increased with increasing temperature. Mean NEP contribution to CO2 emission was 51% and 57% at the non‐perennial and perennial stream, respectively. Although these proportions varied with assumptions about metabolic stoichiometry and groundwater CO2 concentration, in‐stream CO2 production consistently and substantially contributed to total atmospheric CO2 flux in both streams. We conclude that in‐stream metabolism can be more important for driving C cycling in some headwater streams than previously assumed. [ABSTRACT FROM AUTHOR]