In order to reveal the development mechanisms of various newly discovered microtopographies in the Badain Jaran desert region and their implications for water transport and water balance within the megadunes, a range of methods were employed, including field observation, electron microscope identification, X-ray diffraction and laser particle size analyzer. The results indicate the presence of tadpole-shaped microtopography, comb-shaped microtopography, densely distributed sand balls with salt film and multilayered gravitational water on the surface. These microtopographies have not been previously reported, and their distribution within the upper and middle parts of the megadunes is multi-layered and regular. The finer-grained sand layer, where tadpole-shaped microtopography is located, has a higher water content, while the coarser-grained sand layer has a lower water content. The mineral composition of the salt film is principally calcite, with smaller quantities of salt and sulphate. The alternating distribution of finer-grained sand layers with higher water content and coarser-grained sand layers with lower water content is the reason for the multi-row distribution of the tadpole-shaped micro-topography. The formation of tadpole-shaped microtopography can be subdivided into three distinct stages, which develop under four different dynamic conditions. The existence of multiple microtopographies, multiple layers of higher content of water and multiple layers of soluble salts provides robust evidence that this megadune area exhibits a positive water balance. This phenomenon is indicative of atmospheric precipitation that infiltrates the deeper parts of the megadune, resulting in the enrichment of multilayer water within the megadune. Atmospheric precipitation is probably a persistent water source for these lakes, consistent with the widespread spring discharge zones and runoff belts observed along the lake margins. This study is of significant scientific import with regard to the identification of the sources and water cycles of over 140 small lakes in the region, as well as the development of the microtopography.