Abstract. Our ability to predict future climate change relies on our understanding of current and future CO 2 fluxes, particularly on a regional scale (100-1000 km). CO 2 regional sources and sinks are still poorly understood. Inverse transport modeling, a method often used to quantify these fluxes, relies on atmospheric CO 2 measurements. One of the main challenges for the transport models used in the inversions is to properly reproduce CO 2 vertical gradients between the boundary layer and the free troposphere, as these gradients impact on the partitioning of the calculated fluxes between the different model regions. Vertical CO 2 profiles are very well suited to assess the performances of the models. In this paper, we conduct a comparison between observed and modeled CO 2 profiles recorded during two CAATER campaigns that occurred in May 2001 and October 2002 over Western Europe, as described in a companion paper. We test different combinations between a global transport model (LMDZt), a mesoscale transport model (CHIMERE), and different sets of biospheric fluxes, all chosen with a diurnal cycle (CASA, SiB2 and ORCHIDEE). The vertical profile comparison shows that: 1) in most cases the influence of the biospheric flux is small but sometimes not negligible, ORCHIDEE giving the best results in the present study; 2) LMDZt is most of the time too diffuse, as it simulates a too high boundary layer height; 3) CHIMERE better reproduces the observed gradients between the boundary layer and the free troposphere, but is sometimes too variable and gives rise Correspondence to: I. Xueref-Remy (irene.xueref@lsce.ipsl.fr) to incoherent structures. We conclude there is a need for more vertical profiles to conduct further studies to improve the parameterization of vertical transport in the models used for CO 2 flux inversions.Furthermore, we use a modeling method to quantify CO 2 fluxes at the regional scale from a chosen observing point, coupling influence functions from the transport model LMDZt (that works quite well at the synoptic scale) with information on the space-time distribution of fluxes. This modeling method is compared to a dual tracer method (the so-called Radon method) for a case study on 25 May 2001 during which simultaneous well-correlated in situ CO 2 and Radon 222 measurements have been collected. Both methods give a similar result: a flux within the Radon 222 method uncertainty (35%), that is an atmospheric CO 2 sink of −4.2 to −4.4 gC m −2 day −1 . We have estimated the uncertainty of the modeling method to be at least 33% on average, and even more for specific individual events. This method allows the determination of the area that contributed to the CO 2 observed concentration. In our case, the observation point located at 1700 m a.s.l. in the north of France, is influenced by an area of 1500×700 km 2 that covers the Benelux region, part of Germany and western Poland. Furthermore, this method allows deconvolution between the different contributing fluxes. In this case study, the biospheric sink contri...