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The movement of water into soil is the primary driving force in nutrient transport for crops, and the laws governing this movement can be affected by crop roots and plough pans. The main objectives of this study were to monitor the movement of water during rain along a soil profile influenced by soybean roots and a plough pan and to assess whether these factors influenced the efficacy of using the Richards equation to simulate the transport of soil water along a profile associated with a single rain. Experiments and model simulations were carried out. Our results suggested that the soybean field soil may have had preferential flow paths. Soybean stems and leaves transferred rainwater that otherwise would have fallen farther from the central stalk. The transmission of rainwater by the branches and leaves had a larger effect than the interception of rainwater by the branches and leaves. The effect of the root system on the soil particles may increase soil capillary action and ultimately increase saturated hydraulic conductivity. Saturated hydraulic conductivity was higher near the surface than at depth, because the transmission of water by the root system and the effect of large gaps were greater in the soil near the surface. Saturated hydraulic conductivity for both bare land and land covered with soybean plants decreased linearly from depths of 0–15 cm along the soil profile, particularly in the presence of a plough pan. We developed a linear equation to represent the variation in saturated hydraulic conductivity in the 0–15-cm layer in the black soil area of northeastern China. Using our linear model for saturated hydraulic conductivity as a parameter, the Richards equation more accurately simulated soil water transport along a profile influenced by soybean roots and a plough pan in rainy conditions.