The Brazilian semiarid region presents a physical water scarcity and high seasonal and interannual irregularities of precipitation, known as a region with periodic droughts. This region is mainly covered by the Caatinga biome, recognized as a Seasonally Dry Tropical Forest (SDTF). Soil water availability directly impacts the ecosystem's functioning, characterized by low fertility and sparse vegetation cover during the dry season, making it a fragile ecosystem vulnerable to climatic variations. Additionally, this region has been suffering from several issues due to human activities over the centuries, which has resulted in extensive areas being severely degraded, which aggravates the impacts from climatic variations and the susceptibility to desertification. Thus, studying the soil-plant-atmosphere continuum in this region can help better understand the seasonal and annual behavior of the water and carbon fluxes. This study investigated the dynamics of water and carbon fluxes during four years (2013-2016) by using eddy covariance (EC) measurements within two areas of Caatinga (dense Caatinga (DC) and sparse Caatinga (SC)) that suffered anthropic pressures. The two study areas showed similar behavior in relation to physical parameters (air temperature, incoming radiation, vapor pressure deficit, and relative humidity), except for soil temperature. The SC area presented a surface temperature of 3 °C higher than the DC, related to their vegetation cover differences. The SC area had higher annual evapotranspiration, representing 74% of the precipitation for the DC area and 90% for the SC area. The two areas acted as a carbon sink during the study period, with the SC area showing a lower CO2 absorption capacity. On average, the DC area absorbs 2.5 times more carbon than the SC area, indicating that Caatinga deforestation affects evaporative fluxes, reducing atmospheric carbon fixation and influencing the ability to mitigate the effects of increased greenhouse gas concentrations in the atmosphere.