Appropriate tillage and crop diversifications can improve soil quality leading to yield sustainability. Our objective was to quantify tillage, crop rotation and mineral fertiliser application effects on carbon sequestration, aggregation and soil water movement after two cropping cycles in the smallholder sector of Zimbabwe. Two split-plot experiments were set up at four sites on sandy, loamy and clayey soils. At experiment 1, crop rotation (maize-soya bean; continuous maize) was the main plot and mineral fertiliser ((NPKS (180 N + 30P2O5+30K2O+6.5SO3 kg ha−1); control (no fertiliser added)) was the sub-plot. At experiment 2, tillage (reduced, conventional) was the main plot and mineral fertiliser (NPKS; control) was the sub-plot. Soil samples collected from 0 to 0.2 m and 0.2–0.4 m layers were analysed for soil organic matter (SOM) content, bulk density and proportion of water stable aggregates. Saturated hydraulic conductivities (Ks), steady state infiltration rates (is) and soil sorptivities (Sp) were estimated from fitting field infiltration data into the Phillip model. SOM stocks (mean = 3.483 Mg ha−1) were significantly increased by reduced tillage at the sandy site and higher (p < 0.05) in 0–0.20 m than in 0.20–0.40 m layers at clayey sites. Proportion of water stable aggregates increased (p < 0.05) under reduced tillage compared with conventional tillage and under rotation compared with continuous maize system. Bulk densities were 11% lower (p < 0.05) in the 0–0.20 m than in 0.20–0.40 m layers. The estimated Ks(1 × 10−4-8x10−4 cm s−1) and is (7.08–55 × 10−4 cm s−1) were at least 100% higher (p < 0.05) under rotation compared with continuous maize whilst sorptivities (0.050–0.143 cm s−05) did not vary across the treatments. NPKS fertiliser reduced (p < 0.05) is by up to 1.8 fold compared with the control. Short term adoption of reduced tillage and maize-soya bean rotation can mitigate soil structural degradation; increase water recharging and increase carbon sequestration quicker in sands than in the buffering clays making the practices more relevant in the smallholder sector.