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In southern Africa, tillage research has focused on rainfed smallholder cropping systems, while literature on high-input irrigated cropping systems is limited. We evaluated the effects of conventional (CT), minimum (MT) and no-till (NT) tillage systems on soil organic carbon (SOC), bulk density, water-stable aggregates (WSA), mean weighted diameter (MWD) and crop yields in an irrigated wheat-cotton rotation. Soil data were monitored in the first and final year, while yields were monitored seasonally. Average bulk densities (1.5-1.7 Mg m(-3)) were similar among tillage systems, but often exceeded the critical limit (1.60 Mg m(-3)) for optimum root growth. Conversion from CT to MT and NT failed to ameliorate the high bulk densities associated with the alluvial soil. SOC (g kg(-1)) at 0-15 cm was higher (P < 0.05) under MT (3.9-5.8) and NT (4.2-5.6) than CT (2.9-3.3). Corresponding horizon SOC stocks (Mg C ha(-1)) for the tillage treatments were; 9.3-13.9 (MT), 9.3-13.5 (NT) and 7.3-7.7 (CT). In the final year, significant (P < 0.05) tillage effects on SOC stocks were also observed at 15-30 cm. Cumulative SOC stocks (Mg C ha(-1)) in the 0-60 cm profile were higher (P < 0.05) under MT (32.8-39.9) and NT (32.9-41.6) than CT (27.8-30.9). On average, MT and NT sequestered between 0.55 and 0.78 Mg C ha(-1) year(-1) at 0-30 cm depth, but a net decline (0.13 Mg C ha(-1) year(-1)) was observed under CT. At 0-30 cm, MT and NT had higher (P < 0.05) MWD (0.19-0.23 mm) and WSA (2.3-3.5%) than CT (MWD: 0.1-0.12 mm, WSA: a parts per thousand 1.0%). Both MWD and WSA were significantly (P < 0.05) correlated to SOC. Seasonal yields showed significant (P < 0.05) tillage effects, but 6-year mean yields (t ha(-1)) were similar (CT: 4.49, MT: 4.33, NT: 4.32 for wheat; CT: 3.30, MT: 2.82, NT: 2.83 for cotton). Overall, MT and NT improved soil structural stability and carbon sequestration, while impacts on crop productivity were limited. Therefore, MT and NT are more sustainable tillage systems for the semi-arid regions than conventional tillage.