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Effects of continuous cropping, fertilisation, and manuring on soil organic carbon content and physical properties such as particle size distribution, bulk density, aggregation, porosity, and water retention characteristics of a Typic Ustochrept were examined after 31 cycles of maize–wheat–cowpea (fodder) crop rotation. Five contrasting nutrient treatments from a long-term fertiliser experiment were chosen for this study: control (no fertiliser or manure); 100% (optimum dose) nitrogen (N) fertiliser; 100% nitrogen and phosphorus (NP); 100% nitrogen, phosphorus, and potassium (NPK); 100% NPK + farmyard manure (NPK+FYM). The NPK+FYM treatment significantly improved soil organic carbon (SOC) content in 0–0.15 m soil compared with the other 4 treatments; the NPK treatment resulted in significantly more SOC than the control and N treatments (P < 0.05). The SOC in NPK and NPK+FYM treatments was 38.6 and 63.6%, respectively, more than the initial level of SOC (4.4 g/kg) after 31 cycles of cropping. The control and N treatments maintained the SOC status of the soil at the initial value. NPK+FYM significantly improved soil aggregation, soil water retention, microporosity, and available water capacity and reduced bulk density of the soil at 0–0.30 m depth. Greater crop growth under the NPK treatment resulted in increased organic matter content of soil, which improved aggregate stability, water retention capacity, and microporosity compared with the control. The effects were more conspicuous with the NPK+FYM treatment and at the surface soil (0–0.15 m). Application of imbalanced inorganic fertiliser (N and NP treatments) did not have a deleterious effect on the physical properties of the soil compared with the control. SOC content showed a highly significant and positive correlation with mean weight diameter (0.60), % water-stable macro-aggregates (0.61), and soil water retention at –0.033 MPa (0.75) and –1.5 MPa (0.72), and negative correlation with bulk density (–0.70) for the surface 0–0.15 m soil. The study thus suggests that application of balanced mineral fertilisers in combination with organic manure sustains a better soil physical environment and higher crop productivity under intensive cultivation.