Abiotic processes in the subsurface produce and consume CO2 and may significantly contribute to the soil CO2 flux (Fc) in arid regions. However, their contribution to Fc in these environments is poorly understood. We measured the surface and subsurface dynamics of temperature, water vapor, and CO2 during a field experiment over two years in the Negev Desert, Israel. We observed a regular diurnal pattern of soil-atmosphere water vapor exchange over the dry season, which was significantly coupled with Fc. Simulations of Fc using a mechanistic model revealed that diurnal fluctuations in water content, originating from adsorption-desorption cycles, played a major role in driving Fc. This finding suggests that atmospheric water vapor, adsorbed to soil particles at night, supplies water to dissolve gaseous CO2 and can explain the diel pattern of CO2 exchange reported in dry periods. The subsurface measurements show that geochemical processes produce and consume soil CO2 both during the dry summer season and after rainfall, and that this process is concentrated in horizons of carbonate accumulation, which act as hotspots for CO2 redistribution. Our findings further reveal that summer heat waves were associated with net COQ emissions, suggesting that increases in minimum daily air temperature, predicted to be exacerbated by climate change, may amplify COQ emissions from alkaline soils. Overall, pulses of increased microbial CO2 production in the biocrust domain following wetting dominated the total yearly carbon loss of 24.26 gC m-2, while geochemical CO2 consumption act as an important moderator of respiration rates in desert ecosystems.