An intensive aircraft campaign measuring atmospheric CO2 mixing ratios was carried out in the central part of the Ebre watershed on late June 2007 to characterize the CO2 dynamics in the Ebre basin and to calculate the regional cumulative carbon surface flux. CO2 concentrations were obtained from vertical profiles over La Muela (LMU; 41.60°N, 1.1°W) from 900 to 4000 m above the sea level (masl), horizontal transects at ∼2000 m 100 km west from LMU, and continuous measurements at ∼650 masl. Different estimates of surface flux from changes in the convective boundary layer (CBL) CO2 concentration were obtained following the Integral CBL budgeting equation (ICBL) and the carbon content integration (CCI) method. Values of the mean surface flux calculated from the different approaches range from −2.4 to −7.9 μmolCO2/m2s. Regional surface flux calculated from vertical profiling appears to be consistent in a distance of 70 km away from the measurement site. The ICBL method is very sensitive to the accurate determination of the concentration in the entrainment zone. The overall uncertainty from fluxes calculated from the ICBL method rises to a value of 70%, whereas the uncertainty linked to the CCI method is 55%.