The data set contains 5598 measurements of soil CO efflux, 2515 of net ecosystem exchange, soil and air temperature, air moisture, watertable and photosynthetically active radiation (some of points), measured on 76 points in 8 types of bog and forest microlandscapes. The data has been collected during summer seasons (June-August) and partially in other months from 2013 to 2019 in the south taiga paludified forest and bog ecosystems of European Russia, within the Central Forest Biosphere Reserve. Aim of the study was to determine the contribution of individual microform types to the spatio-temporal dynamics of CO2 fluxes under different types of oligotrophic waterlogging. Measured by chamber method flux values (soil respiration (R), mg/m2/h) are integral CO₂ emission values, i.e. autotrophic + heterotrophic respiration. Net ecosystem exchange (NEE, mg/m2/h) is the balance of soil and aboveground plant cover is the difference between CO2 emission and deposition of carbon dioxide in the photosynthetic process. The negative sign of the balance corresponded to the uptake of CO2 from the atmosphere. Detailed objects and methods are described in (Ivanov et al., 2017. doi:10.1134/S1995425517020056; Ivanov et al., 2019. doi:10.1007/s11676-019-00963-4).