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Deserts are groundwater-dependent ecosystems. Modern rainfall appears to recharge groundwater in the deserts, but direct observations are lacking. Desert pavements (DPs) and gilgai microtopography are typical landform in arid deserts. Here, we investigated whether DPs and gilgai microtopography resulted in groundwater recharge. We used photos and videos, measurements of water table fluctuations, and groundwater hydrochemistry. Research findings showed that DPs and gilgai microtopography formed and captured runoff after a heavy rain. The rise of both water table and trace ion concentration in groundwater demonstrated that gilgay microtopography recharge groundwater by collecting rainfall after a heavy rain in the arid Gobi Desert. We concluded that DPs and gilgai synergistically captured rainfall and then recharged groundwater in arid Gobi Deserts. This study provides evidence to support the viewpoint of groundwater recharge by rainfall in arid deserts.