The carbon balance in forest ecosystems is represented by the net primary production, which is defined as the difference between the chemical energy fixed by photosynthesis and the loss between heterotrophic and autotrophic respiration and mortality. Understanding these components and the factors that regulate the species is critical to predicting the effects of the environment on plant growth. The objective of the present study was to investigate the CO2 and water vapor exchanges in plant organs from integrated canopies and by measurements on the soil, continuously and specifically evaluating the temporal variations and the effects of climate seasonality on eucalyptus plantations at different ages. For this purpose, we utilized tools for high-frequency data collection by the isotope ratio and eddy-covariance system techniques present in two micrometeorological towers in eucalyptus plantations located in the Central-West region of Brazil, more specifically in the state of Mato Grosso do Sul. Soon after planting, a growing increase in the absorption of CO2 from the atmosphere was observed, indicating that the plant increased its carbon fixation. At younger ages they presented higher fixation rates, determined by the gross primary productivity and respiration of CO2 most likely accumulated due to the more accelerated growth, verified by the greater biomass increments. Higher CO2 flows were found in the leaves and roots at these ages. In the adult age, CO2 flows presented a marked increase over time, reduced in the dry season; as in the young plantations, the leaves accounted for respiratory activity. Response of the plant to the climate was demonstrated by its increased CO2 flow, and the highest daily values for net photosynthesis rate, stomatal conductance and transpiration were observed in the periods of greater water and energy availabilities. Climatic seasonality was also found to affect the biometric measurements of the leaf area index and specific leaf area. In dry periods, the young plantation more efficiently utilized water than the adult plantation, which facilitates acclimatization of the plant to allow for carbon incorporation to continue, avoiding excessive water loss. Measures of soil respiration showed to be correlated with the soil temperature, and they were also affected by the soil water content. When comparing the result generated by the influence of climate on the isotope ratio (δ13C) of the air flows, we observed that the plant organs and the soil generally showed greater discriminations in the rainy season. There were no statistical differences between the δ13C of any of the organs evaluated in the young and adult plantations during the rainy season. This result differs for the leaves and branches in the dry season. The partitioned contribution of the autotrophic and heterotrophic individuals generated from the δ13C values in a mixed analysis suggested that 51.7% is related to the aerial part of the ecosystem, and thus 48.3% is from respiration of the soil and its components. The adopted methodologies contributed to better understanding of the carbon balance and the soil-plant- atmosphere relation, and showed to efficiently evaluate the sources that contribute to the air flow in eucalyptus ecosystems.