Headwater streams are control points for carbon dioxide (CO 2 ) emissions to the atmosphere, with relative contributions to CO 2 emission fluxes from lateral groundwater inputs widely assumed to overwhelm those from in-stream metabolic processes. We analyzed continuous measurements of stream dissolved CO 2 and oxygen (O 2 ) 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 CO 2 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 CO 2 and O 2 concentrations, and a strong correlation between aerobic ecosystem respiration (ER) and gross primary production (GPP) despite persistent negative NEP. At the perennial stream, the CO 2 -O 2 relationship varied largely over time, ER and GPP were uncorrelated, and NEP, which was consistently negative, increased with increasing temperature. Mean NEP contribution to CO 2 emission was 51% and 57% at the non-perennial and perennial stream, respectively. Although these proportions varied with assumptions about metabolic stoichiometry and groundwater CO 2 concentration, in-stream CO 2 production consistently and substantially contributed to total atmospheric CO 2 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.Streams and rivers are control points in global carbon (C) cycling because of high carbon dioxide (CO 2 ) emission rates (Caraco and Cole 2003;Cole et al. 2007;Drake et al. 2018). High emissions from small streams are attributed principally to groundwater inputs of dissolved CO 2 from soil organic matter decomposition (