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 active trace gases (e.g., CH₄, CO) in the same framework. We assess the performance of this new system in a pseudodata experiment that resembles the real problem we will apply this system to. The sensitivity of the method to the choice of several parameters such as the assimilation window size and the number of ensemble members is investigated. We conclude that the system is able to provide satisfactory flux estimates for the relatively large scales resolved by our current observing network and that the loss of information in the approximated covariances is an acceptable price to pay for the efficient computation of a large number of surface fluxes. The full potential of this data assimilation system will be used for near–real time operational estimates of North American CO₂ fluxes. This will take advantage of the large amounts of atmospheric data that will be collected by NOAA-CMDL in conjunction with the implementation of the North American Carbon Program (NACP).