CO2 fluxes for the Netherlands and surroundings are estimated for the year 2008, from concentration measurements at four towers, using an inverse model. The results are compared to direct CO2flux measurements by aircraft, for 6 flight tracks over the Netherlands, flown multiple times in each season. We applied the Regional Atmospheric Mesoscale Modeling system (RAMS) coupled to a simple carbon flux scheme (including fossil fuel), which was run at 10 km resolution, and inverted with an Ensemble Kalman Filter. The domain had 6 eco-regions, and inversions were performed for the four seasons separately. Inversion methods with pixel-dependent and -independent parameters for each eco-region were compared. The two inversion methods, in general, yield comparable flux averages for each eco-region and season, whereas the difference from the prior flux may be large. Posterior fluxes co-sampled along the aircraft flight tracks are usually much closer to the observations than the priors, with a comparable performance for both inversion methods, and with best performance for summer and autumn. The inversions showed more negative CO2 fluxes than the priors, though the latter are obtained from a biosphere model optimized using the Fluxnet database, containing observations from more than 200 locations worldwide. The two different crop ecotypes showed very different CO2uptakes, which was unknown from the priors. The annual-average uptake is practically zero for the grassland class and for one of the cropland classes, whereas the other cropland class had a large net uptake, possibly because of the abundance of maize there.