The main objective of this study was to evaluate meteorological variables and the simulated components of energy and CO2 balances in desertification hotspots in Northeast Brazil. Meteorological data were obtained from the National Institute of Meteorology measurement network for the Cabrobó and Ibimirim sites. Initially, hourly linear trends were calculated for the meteorological variables using the non-parametric Mann–Kendall test. Then, the seasonal variability in the components of energy and CO2 balances was assessed through simulations of the simple tropical ecosystem (SITE) model. Results showed evidence of increasing air temperature trends in the Cabrobó site in the first months of the year, which was not observed in the Ibimirim site. Regarding relative humidity, increasing trends were observed in a few months over the Cabrobó site, while decreasing trends were observed in the Ibimirim site. Opposite behaviors were also identified for the trends in wind speed in both sites. Gross primary production (GPP) and net ecosystem exchange (NEE) simulated values were higher in the first half of the year in both sites. GPP varied from 0.8 to 1.2 g C m−² h−¹, and NEE fluctuated around approximately −5 g C m−² h−¹. These results indicate that rainfall seasonality is a crucial factor for the modulation of CO2 and energy balance fluxes in the Caatinga biome.