Urmia Lake is a large-scale hypersaline lake that experienced a drastic water-level fall due to natural and anthropogenic forces during the last two decades. Construction of a causeway in the central part of the lake after 1989 has divided the lake into northern and southern parts and caused an extreme change of the lake hydrochemical system. Precipitation of evaporite minerals as crust on the lake floor was caused by the combination of lake level fall and increasing water salinity. However, some parameters controlling rates of salt deposition and dissolution and temporal and spatial variation in salt thickness in Lake Urmia are poorly understood. This study reviews 90 sediment cores from various parts of the lake to put forward a better understanding of the salt depositional system and salt thickness variations in the basin for the last 40 years (1977–2017). Our results indicate that the sedimentary system of Urmia Lake changed rapidly during the last two decades from a permanent hypersaline lake with predominantly fast terrigenous–biochemical sedimentation to a seasonally changing playa sedimentary environment with predominance of evaporite minerals. These changes are responsible for rapid salt deposition that generated a salt-crust with a maximum thickness of 2.95 m overlying Holocene terrigenous sediments. The salt-crust thickness and the water depth have a positive correlation for water depth greater than 1 meter, which means that salt-crust thickness increases where water depth increases. While the thickness of shallow deposits are affected by fresh-water dissolution. In addition, the average salt precipitation rate in the northern and the southern parts of the lake is 466 and 266 times higher, respectively, than the average (0.3 mm/y) sedimentation rate before the lake shrinkage. Similar to other large hypersaline lakes such as the Great Salt Lake (USA) and the Aral Sea (Central Asia), the manmade intervention at Urmia Lake (damming of the catchment, extension of agricultural fields, and causeway construction in the middle part of the lake) threatens its further hydrologic existence.