Soil aggregate stability and organic carbon (OC) storage are key biogeochemical indicators of soil health, and their ability to function within an ecosystem includes providing sustainable and just media for the transformation of agri-food systems. Soil aggregation protects OC, and its disruption through natural or human activities can lead to OC loss. While land use impacts soil quality, its effect on aggregate stability and OC stocks in Botswana's agriculturally important Pandamantenga alluvial plains is not well understood. This study assessed the influence of four distinct land uses—arable land (subject to tillage and mechanical disturbance), grassland exclosures (areas protected from grazing to allow vegetation recovery), natural exclosures (undisturbed areas with minimal human intervention), and pastures (grazed rangeland) on soil structure and carbon dynamics. Soil samples were collected at three depths (0–15, 15–30, and 30–45 cm) and sieved into six aggregate size classes (>4.75, 4.75–2.00, 2.00–1.00, 1.00–0.50, 0.50–0.25 and <0.25 mm). Routine laboratory methods, including particle size, bulk density, pH, electrical conductivity, exchangeable bases, OC content, and aggregate-associated carbon, were used to analyse the soil properties. Aggregate stability was assessed via wet sieving, and indices such as water-stable aggregate (WSA), mean weight diameter (MWD), geometric mean diameter (GMD), and R0.25 were calculated. The results revealed that land use significantly affected the soil structure and carbon dynamics. The natural exclosures presented the highest MWD and GMD, followed by the grassland exclosures, pastures, and arable land. The WSA varied by land use and aggregate size, with arable land having more WSA in smaller fractions and less WSA in larger fractions. Pastures had more mid-sized aggregates, whereas natural exclosures were dominated by larger aggregates. R0.25 remained consistent across land uses because of the high clay content. Larger aggregates (>0.25 mm) contained more OC and showed a strong positive correlation between stability and OC, highlighting the importance of v aggregate stability for carbon sequestration and soil health by minimizing carbon loss and enhancing SOC storage. The natural exclosures had the highest OC stocks, particularly in the larger aggregates, followed by the arable land. Grassland exclosures and pastures had lower OC stocks. These findings will inform strategies to improve sustainable agricultural productivity, soil conservation, and carbon management in the face of climate change.