In hyper-arid regions, soil moisture’s role in ecohydrological processes can differ significantly from that in arid or semi-arid ecosystems. We investigated the spatial–temporal dynamics of soil moisture and its relationship with groundwater depths in a 200 m × 300 m phreatophytic tamarisk stand in the lower basin of the Tarim River, a hyper-arid zone in China. Soil moisture profiles, from the surface to the water table, were derived using drilling and oven-drying techniques. Over a three-year period, the soil moisture at multiple depths was continuously monitored in a specific plot using nine frequency domain reflectometry (FDR) sensors. Our results indicate a correlation between horizontal variations in soil moisture and groundwater depths (GWDs). Nevertheless, anomalies in this correlation were observed. Variations in horizontal soil moisture were strongly influenced by the clay content in the soil, with finer soils retaining more moisture. Despite varying GWDs, soil moisture profiles remained consistent, with no distinct correlation between them. Soil moisture exhibited stability across layers, with noticeable changes only adjacent to the water table. These results imply that in hyper-arid environments, soil texture primarily governs soil moisture distribution. However, the limited spatial and temporal scopes in our dataset, constrained by the region’s inhospitable conditions, necessitate further investigation. Future work should prioritize amalgamating diverse data sources to devise a region-specific soil moisture model for in-depth analysis of hyper-arid regions.