Temporal scales of variability for the partial pressure of CO₂ (pCO₂) in the surface waters of two stratified Mediterranean reservoirs were examined through the temporal decomposition of 5 month time series with hourly sampling frequency. pCO₂ time series included similar patterns of variability at daily, biweekly, and seasonal scales regardless of the difference in amplitude of the pCO₂ variation in the two reservoirs studied. Daily variability was strongly related to the day-night cycles of metabolic activity, accounting for about one third of the total amplitude in pCO₂ variation. At a biweekly scale, wind forcing led to higher rates of air-water CO₂ exchange and subsequently temporary partial mixing events associated to relevant increase of CO₂ concentration in surface waters. Seasonal variability accounted for one third of the amplitude of the pCO₂ variability and was coupled to the seasonal dynamics of water temperature and thermal stratification of the water column. Our results provide evidence that CO₂ emission from stratified water bodies shows significant variability at daily, biweekly, and seasonal scales; all of which should be taken into consideration in the analyses of the carbon fluxes. The wind-induced mixing events, operating at temporal scales between daily and seasonal cycles, may become a major factor controlling the pCO₂ dynamics. Hence, some of the most common models for computing CO₂ fluxes from pCO₂ were not able to reproduce the biweekly response patterns of CO₂ emissions to wind forcing.