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Seasonal changes of the soil CO2 concentration and the rate of CO2 fluxes emission from the soil formed on the sediments of the former Lake Texcoco, which occupied a significant part of the Mexico Valley until the mid-17th century, were studied. The soils (Fluvic Endogleyic Phaeozems) were characterized by a low CO2 fluxes rate, which is related to their high alkalinity. The mean values of soil respiration were 6.0–14.1 mg C/(m2 h) depending on vegetation type, which corresponds to 60–157 g C/(m2 yr). The contribution of plants to the CO2 fluxes insignificantly varied by seasons and depended on the species composition of vegetation. The soil CO2 concentration and soil respiration in eucalypt (Eucalyptus globulus Labill.) plantation were two times higher than those in the grass–subshrub area, the ground cover of which consisted of Distichlis spicata (L.) Greene and Suaeda nigra (Raf.) J.F. Macbr. species. This can be related to the significant volumes of gas production during the respiration of eucalypt roots and associated rhizosphere community. The contribution of the root systems of grass cover to the soil CO2 fluxes in eucalypt plantation slightly varied within the year and was equal to 24% on the average. In the grass–subshrub area, its value varied from 41% in the cold season to 60% in the warm season. The spatial variability of soil CO2 concentration and its flux rate to the atmosphere was due to the differences in plant species composition and hydrothermal conditions, and their temporal trend was closely related to the seasonal accumulation of plant biomass and soil temperature.