CO<inf>2</inf> 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 CO<inf>2</inf> flux 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 CO<inf>2</inf> 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 CO<inf>2</inf> uptakes, 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. © 2012. American Geophysical Union. All Rights Reserved.