An understanding of how boreal forest composition responds to global environmental changes is an important challenge to predicting the future global carbon balance. Boreal forests are the most significant sink for atmospheric carbon dioxide; however, their sequestration capacity is highly sensitive to ongoing climate changes. The combination of the hydrothermal conditions of a territory strongly regulates its biogeochemical processes. The carbon fluxes in boreal forests are strongly mediated by the ground vegetation cover, composed of mosses (mesic) and lichens (xeric). Despite the concurrence of xeric and mesic vegetation types, their responses to climate variations varies significantly. Soil emission is an informative indicator of ecosystem functioning. In this study, we focused on the soil CO2 dynamics during frost-free seasons with different precipitation regimes in the xeric and mesic boreal ecosystems of Central Siberia. Seasonal measurements of soil CO2 emissions were conducted during frost-free seasons using the dynamic chamber method. Our findings reveal that the precipitation regimes of each year may control the seasonal soil emission dynamics. The soil moisture is the most important driver of emissions growth in the water-limited lichen pine forest (R2adj. = 18%). The soil temperature plays the largest role in the feather moss pine forest during the dry (R2adj. = 31%) seasons, and in the lichen pine forest during the wet (R2adj. = 41%) seasons. The cumulative efflux for the xeric and mesic sites is mostly related to the hydrothermal conditions, and not to the differences in ground vegetation cover. During the dry seasons, on average, the soil CO2 emissions are 45% lower than during the wet seasons for both sites. These findings emphasize the need for estimating and including the hydrothermal characteristics of the growing season for detailed emission assessments.