Understanding the variability in water availability in agroforestry systems in rain-fed orchards is vital for optimizing orchard management in semiarid areas. However, few studies have examined the soil capacity of water stock and supply in these systems over multiple years. We aim at (i) characterizing several soil physical properties related to water availability and inter-annual dynamics of soil water content and (ii) exploring their response to meteorological conditions and root distribution. Jujube (Ziziphus jujuba Mill.) intercropped with the fodder species canola (Brassica napus L.) (JFCS), jujube intercropped with daylily (Hemerocallis fulva L.) (JDLS), and a jujube orchard with clean tillage (JCS) were established on the Loess Plateau, China. Soil physical properties (including soil bulk density, soil hydraulic conductivity, soil field capacity, and soil porosity), soil water content and fine root data were collected over the period 2014–2017. Compared to JCS-Tree, the field capacity was significantly increased both in the JFCS-Tree and JDLS-Tree treatments, while soil capillary porosity increased significantly only in the JFCS-Tree. Compared to JCS-Inter-row, the JFCS-Inter-row and JDLS-Inter-row exhibited significantly decreased soil bulk density, and increased field capacity, saturated hydraulic conductivity, and improved soil porosity, but the non-capillary porosity in the JDLS-Inter-row treatment were not significantly modified. Compare to JCS-Tree treatment, the soil water at 0–60 cm significantly increased under JFCS-Tree and JDLS-Tree in four years. However, due to the deeper fine root distribution for both tree and crop under JDLS-Inter-row, the soil water content at 60–180 cm in JDLS-Inter-row significantly decreased more than JFCS-Inter-row and JCS-Inter-row. The introduced crop modified the soil physical properties and soil water content, indirectly under trees and directly between inter-rows through the role of fine roots, thereby changing the orchard environment in semiarid areas. Agroforests can generally improve water condition at shallow soil layers compared to monocultural plantations, although such an effect may be accompanied with lower water stock at deeper soil layers in inter-rows, depending on crop species chosen.