Adequate knowledge of tempo-spatial variability on soil hydraulic properties plays an important role in irrigation scheduling and precision farming. This study was conducted to compare the impact of tempo-spatial variations in long-term conservation tillage applications in organic farming (superficial tillage using a chisel at 10 cm depth) on soil properties. Soil measurements, including infiltration capacity, saturated hydraulic conductivity (Ks), effective bulk density, and penetration resistance, were investigated in 2012 and compared to data from 2008 at the same fields in Baden-Württemberg, Germany. Long-term organic farming reflected a relative increase in Ks values with temporal variability 33% more in 2012 than in 2008, while soil texture was virtually time-invariant. The Ks increased from 27.06, 24.42, 40.46, 17.49, and 22.59 cm d−1 in 2008 to 33.17, 28.79, 47.75, 38.99, and 40.82 cm d−1 in 2012 for sample locations I, II, III, IV, and V, respectively. The effective bulk density values decreased from 1.72, 1.72, 1.68, 1.64, and 1.81 Mg m−3 in 2008 to 1.63, 1.56, 1.67, 1.32, and 1.48 Mg m−3 in 2012 for sample locations I, II, III, IV, and V, respectively. For spatial variations within the same season, variances in computed Ks values were attributed to differences in the soil textures and effective bulk density between different parcels. As the soil was managed by organic farming for a long time, the soil depth compactness was more pronounced in 2012 than in 2008. Nevertheless, the Ks values showed a temporal increase from 2008 to 2012 due to the preferential water flow pathways approach used in organic farming. Estimated Ks values by the Hydrus-1D model in 2012 were five times higher than in 2008. With soil depth, Ks values revealed a decreasing trend over time. Using the numerical model, Hydrus-1D was representative for comparing hydraulic parameters and simulating water transfer in the soil matrix