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The Badain Jaran Desert exhibits the greatest difference in altitude of all of the world’s deserts. On the slopes of megadunes in the desert, there are physical and chemical deposits produced by surface runoff. In addition, we have observed rarely-seen infiltration-excess surface runoff in the megadune depressions as well as spring streams at the base of megadunes. We used electron microscopy, energy spectrum analysis, infiltration experiments, moisture content determinations and grain-size analysis to study the mineral and chemical composition of the runoff precipitates, and grain-size of the deposits associated with the runoff, together with the hydrological balance in the megadune area, and the atmospheric precipitation mechanism responsible for groundwater recharge and for supplying water to lakes. The observations of shallow runoff and infiltration-excess surface runoff indicate the occurrence of strong and effective precipitation in summer, which would provide an important source for groundwater recharge. Several lines of evidence, such as the physical and chemical deposits resulting from shallow subsurface runoff, spring streams, infiltration-excess runoff, and gravity capillary water with a moisture content of 3-6%, demonstrate that precipitation reaches the base of the megadunes through infiltration and subsequently becomes groundwater. The chemical deposits, such as newly-formed calcite and gypsum, and gray-black physical deposits, as well as different stages in the development of fan-shaped landforms resulting from shallow subsurface runoff, indicate that groundwater recharge in the area is the result of long-term precipitation, rather than intermittent individual major rainfall events. Fine sand layers with a low infiltration capacity lead to subsurface runoff emerging at the ground surface. Five factors play an important role in maintaining a positive water balance and in replenishing groundwater via rainfall: effective rainfall as a water source, the high infiltration capacity of the sands enabling rainfall to rapidly become capillary water in the dunes, low evapotranspiration rates due to the sparse vegetation, the fact that the depth of the sand layer influenced by evaporation is shallow enough to maximize the deep infiltration of rainfall, and rapidly-moving gravity capillary water in the sandy dunes. These five factors together constitute a mechanism for groundwater recharge from rainfall, and explain the origin of the groundwater and lakes in the area. Our findings represent a significant advance in research on the hydrological cycle, including groundwater recharge conditions and recharge mechanisms, in this desert region.