Polygonal networks occur on various terrestrial and extraterrestrial surfaces holding valuable information on the pedological and climatological conditions under which they develop. However, in contrast to their periglacial counterparts, the information that polygons in the hyper-arid Atacama Desert can provide is little understood. To gain insights into their geometrical and geochemical build-up, we performed a morphometric terrain characterization in combination with geochemical and sedimentological analysis on four polygonal networks in the Yungay area of the Atacama Desert. The polygons are composed of siliciclastic sediment that is mainly cemented by sulfates in ~0–50 cm depth and by nitrates and chlorides in ~50–100 cm depth while being separated by about 1 m deep, salt-poor and V-shaped sand wedges. The high salt content (>60 wt%) and high surface temperature variations make a thermal contraction origin likely. The low clay content (~2 wt%) makes an exclusive desiccation origin less relevant but a formation based on dehydration of sulfates remains conceivable. Morphometric data indicate a link between topography and polygon geometry, as the flat-centered polygons (mean size ~4 m) are aligned either in slope direction or perpendicular to it, while being more elongated on steeper slopes. Erosion of these networks is mainly eolian-driven, but we also find signs for aqueous resurfacing of microtopography by fog and minimal rainwater infiltration. Our findings provide a basis for future polygon research in hyper-arid environments, such as Mars, while allowing for the use of polygons as environmental proxies in the Atacama Desert that indicating saline soils and hyper-arid conditions.