The groundwater level in the Wuhai area, which is the most arid area in the northwestern Ordos Basin, has continuously risen in recent years. The groundwater overflows to the surface and forms small lakes, causing the foundations of the houses of local residents to be immersed by water. Through analysis of the isotopes and hydrochemical compositions in the seepage, groundwater, surface water, and precipitation across the Wuhai area, and based on water balance analysis and geological structural features, the reasons for the groundwater level rise of the study area are examined. The results show that the deuterium and oxygen isotopic compositions of precipitation and groundwater in the Wuhai area are not scattered along the same evaporation line, indicating that the groundwater is not recharged by local precipitation. The groundwater in the north-south trending fault zone(ρ(TDS)<1 g/L)in the Wuhai area is more enriched in deuterium and oxygen isotopes than that in the west-east trending fault zone. These characteristics are in accordance with those of the overflowing water in the Wuhai area, suggesting that the rise of the groundwater level is caused by the overflowing water in the north-south trending fault zone. Analysis of ³He/⁴He and ³H in the groundwater of the Ordos Basin shows that the high-conductivity and low-velocity layer in the lithosphere may be the drainage structure of deep-circulating groundwater.