| Summary: | We present a modeling tool capable of computing carbon dioxide (CO<sub>2</sub>) fluxes over a non-uniform boreal peatland. The three-dimensional (3D) hydrodynamic model is based on the “one-and-a-half” closure scheme of the system of the Reynolds-Averaged Navier–Stokes and continuity equations. Despite simplifications used in the turbulence description, the model allowed obtaining the spatial steady-state distribution of the averaged wind velocities and coefficients of turbulent exchange within the atmospheric surface layer, taking into account the surface heterogeneity. The spatial pattern of CO<sub>2</sub> fluxes within and above a plant canopy is derived using the “diffusion–reaction–advection” equation. The model was applied to estimate the spatial heterogeneity of CO<sub>2</sub> fluxes over a non-uniform boreal ombrotrophic peatland, Staroselsky Moch, in the Tver region of European Russia. The modeling results showed a significant effect of vegetation heterogeneity on the spatial pattern of vertical and horizontal wind components and on vertical and horizontal CO<sub>2</sub> flux distributions. Maximal airflow disturbances were detected in the near-surface layer at the windward and leeward forest edges. The forest edges were also characterized by maximum rates of horizontal CO<sub>2</sub> fluxes. Modeled turbulent CO<sub>2</sub> fluxes were compared with the mid-day eddy covariance flux measurements in the southern part of the peatland. A very good agreement of modeled and measured fluxes (R<sup>2</sup> = 0.86, <i>p</i> < 0.05) was found. Comparisons of the vertical profiles of CO<sub>2</sub> fluxes over the entire peatland area and at the flux tower location showed significant differences between these fluxes, depending on the prevailing wind direction and the height above the ground.
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