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Adequate prediction of the spatial and temporal redistribution of greenhouse gas (GhG) within the atmospheric surface layer requires sophisticated process-based models describing the GhG atmospheric transfer, anthropogenic emission and GhG release and uptake by various terrestrial and marine ecosystems. The three-dimensional hydrodynamic model developed in this study allows describing the turbulent transfer of carbon dioxide (CO2) within the atmospheric surface layer taking into account the horizontal land surface heterogeneity including complex topography, mosaic vegetation and soil properties. The model is based on the ”one and a half" E-w closure scheme for the system of the averaged Navier-Stokes and continuity equations, allowing to obtain the established spatial distribution of the average wind speed and turbulent exchange coefficient patterns taking into account horizontal vegetation, soil and surface topography heterogeneity. The spatial distribution of CO2 within the atmospheric surface layer is described using the diffusion-reaction-advection equation (or system of equations) taking into account the spatial distribution of the natural CO2 sources and sinks. The model considers carbon dioxide released by soil and non-photosynthetic parts of plants, and vegetation uptake by plant leaves due to photosynthesis processes in daylight hours. The obtained spatial pattern of CO2 distribution is used to describe the spatial patterns of turbulent and advective CO2 fluxes. The developed model was applied to describe the spatial wind and atmospheric CO2 flux distribution in a non-uniform forest peatland ecosystem in Central part of European Russia. The modeling results were compared with results of CO2 flux measurements conducted using the eddy covariance technique and showed very good agreement.