Based on data collected over five years of monitoring the Lower Tarim River, we analyzed the variability of soil moisture content (SMC) and the relationship between SMC, groundwater table depth (GWD) and vegetation by using the methods of coefficient of variation (Cv), Pearson correlation and regression. The results of the variability of SMC indicate that it rose with increase in depth of soil layer – SMC in the soil layer of 0–60 cm was relatively small compared to SMC in the soil layer of 100–260 cm which showed a significant increase in variability. SMC and GWD before and after ecological water diversions exhibited significant differences at the site of the Yingsu transect and its vicinity of the watercourse, especially SMC in the soil layer of 100–260 cm increased significantly with a significant rise of GWD and reached maximum values at a GWD of about 4 m. Plant coverage and species diversity significantly improved with increases in SMC in the soil layer of 100–260 cm, both of them approached the maximum values and 92.3% of major plant species were able to grow when SMC was > 10%. To restore the ecosystem of desert riparian forest along the Lower Tarim River, the GWD must be maintained at < 4 m in the vicinity of the watercourse and at about 4 m for the rest of this arid region.