Paired eddy covariance site reveals consistent net C sinks over three growing seasons in an African arid and grassy shrubland

• African arid and grassy shrubland site reveals consistent net C sinks over three growing seasons. • Savanna site more productive but has lower and more variable water use efficiency than Nama-Karoo site. • Soil moisture observed as a key factor in modulating the relationship between nighttime respiration and soil temperature at both sites. Anthropogenic climate change and rising atmospheric CO₂ concentrations have the potential to alter ecosystem functioning and land–atmosphere interactions in African drylands. Recent studies suggest that arid ecosystems may respond more positively to these drivers—particularly in terms of primary productivity and water-use efficiency—than previously assumed. We applied a paired-site eddy covariance approach to quantify carbon, water, and energy fluxes across two contrasting dryland vegetation types—the Savanna and Nama-Karoo biomes—located 4 km apart within the Benfontein Nature Reserve, South Africa. Over a 33-month period, distinct diurnal and seasonal differences in the phase and magnitude of carbon fluxes were observed between sites. Cumulative net ecosystem exchange (NEE) was -567 g C m⁻² y⁻¹ at the Savanna site (mean NEE: -189 g C m⁻² y⁻¹) and -160 g C m⁻² y⁻¹ at the Nama-Karoo site (mean NEE: -53 g C m⁻² y⁻¹), indicating higher carbon sequestration in the Savanna. Soil moisture strongly modulated the relationship between nighttime respiration and soil temperature, with reduced microbial temperature sensitivity (lower Q₁₀) once moisture exceeded intermediate levels. In addition, intermediate soil moisture conditions were associated with higher carbon uptake at both sites. Overall, ecosystem water-use efficiency was higher at the Nama-Karoo site but more variable at the Savanna site, potentially due to post-wildfire tree mortality. Sensible and latent heat fluxes followed expected seasonal trends related to radiation and moisture availability. Energy balance closure was greater at the Savanna site (96 %) compared to the Nama-Karoo (80 %), with respective energy balance ratios of 0.93 and 0.88.