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• Manure rate had little influence on the improvement of soil physical properties. • Improvement in soil gas transport and Ksat by manure varied with soil and crop type. • Silty soil had better improvements by manure addition than sandy and clayey soil. Manure application and crop rotation are common agricultural practices that can alter soil physical properties and affect soil functions. In this study, we assessed the effect of long-term manure fertilization (24 to 126 years) and crop type on soil hydraulic, aggregate and pore structural properties. Samples were collected from three long-term experiments (LTEs) in Sweden (silty clay, SiC), Germany (silt loam, SiL) and Denmark (sandy loam, SL). Measurements included water retention, air permeability and gas diffusivity measured at five matric potentials −3, −5, −10, −30 and −50 kPa, saturated hydraulic conductivity (K sat), bulk density (ρ b), and water-stable aggregates (WSA). The treatments at the three LTEs included various manure rates and crop sequences (winter wheat, maize, spring barley, and grass/clover). Results showed that long-term manure addition reduced ρ b by an average of 3–6% for all three sites, and improved soil water retention, plant available water and WSA for most investigated plots. However, increasing manure rates for the SiL and SL sites did not result in further improvements in soil water retention, ρ b and water-stable aggregates. The effect of manure on soil pore size distribution, gas transport, and K sat varied with soil and crop type. Manure increased the porosity of pores < 30 µm in the two fine-textured sites and increased the porosity of pores > 30 µm for wheat and maize plots in the SL site. Manure improved gas transport and K sat in the wheat plots and decreased these properties in the barley plots regardless of soil texture. The maize plots in the SL site had well developed pore structure, while the pore structure in the SiL site was relatively poor. Grass plots had poorer gas transport than maize plots in the SL site despite the manure addition. The study shows that improvements in soil physical and chemical properties arising from manure application largely depend on the crops grown and the soil texture. [ABSTRACT FROM AUTHOR]