We present a data assimilation system to estimate surface fluxes of CO2 and other trace gases from observations of their atmospheric abundances. The system is based on ensemble data assimilation methods under development for Numerical Weather Prediction (NWP) and is the first of its kind to be used for CO2 flux estimation. The system was developed to overcome computational limitations encountered when a large number of observations are used to estimate a large number of unknown surface fluxes. The ensemble data assimilation approach is attractive because it returns an approximation of the covariance, does not need an adjoint model or other linearization of the observation operator, and offers the possibility to optimize fluxes of chemically...