The Siberian region is still sparsely covered by ecosystem observatories, which motivates the exploitation of existing data sets to gain spatially and temporally better-resolved carbon budgets. The Zotino Tall Tower Observatory (ZOTTO; 60°48' N, 89°21' E) observations of CO₂ and CH₄ mole fractions as well as meteorological parameters from six different heights up to 301 m allow for an additional estimate of surface–atmosphere fluxes of CO₂ and CH₄ for the middle Siberian region beginning 2009. The total carbon flux is calculated from the storage and the turbulent flux component. The gradients between the different tower levels determine the storage flux component, which dominates the regional fluxes, especially during nighttime. As a correction term, the turbulent flux component was estimated by the modified Bowen ratio method based on the sensible heat flux measurements at the top of the tower. The obtained average nighttime fluxes (23:00 to 04:00 local time) are 2.7 ± 1.1 μmol (m² s)⁻¹ for CO₂ and 5.6 ± 4.5 nmol (m² s)⁻¹ for CH₄ during the summer months June–September in 2009 and 2011. During the day, the method is limited due to numeric instabilities because of vanishing vertical gradients; however, the derived CO₂ fluxes exhibit reasonable diurnal shapes and magnitudes compared to the eddy covariance technique, which became available at the site in 2012. Therefore, the tall tower data facilitate the extension of the new eddy covariance flux data set backward in time. The diurnal signal of the CH₄ flux is predominantly characterized by a strong morning transition, which is explained by local topographic effects.