© 2011 American Geophysical UnionA regional variational inverse modeling system for the estimation of European biogenic CO2 fluxes is presented. This system is based on a 50 km horizontal resolution configuration of a mesoscale atmospheric transport model and on the adjoint of its tracer transport code. It exploits hourly CO2 in situ data from 15 CarboEurope-Integrated Project stations. Particular attention in the inversion setup is paid to characterizing the transport model error and to selecting the observations to be assimilated as a function of this error. Comparisons between simulations and data of CO2 and 222Rn concentrations indicate that the model errors should have a standard deviation which is less than 7 ppm when simulating the h...