The Dead Sea is located in the Dead Sea Rift, which is part of a long fissure in the Earth's surface called the Great Rift Valley. The 6,000 km (3,700 mile) long Great Rift Valley extends from the Taurus Mountains of Turkey to the Zambezi Valley in southern Africa. The Great Rift Valley formed in Miocene times as a result of the Arabian Plate moving northward and then eastward away from the African Plate.

Around three million years ago what is now the valley of the Jordan River, Dead Sea, and Wadi Arabah was repeatedly inundated by waters from the Red Sea. The waters formed in a narrow, crooked bay which was connected to the sea through what is now the Jezreel Valley. The floods of the valley came and went depending on long scale climatic change. The lake that occupied the Dead Sea Rift, named "Lake Sodom", deposited beds of salt, eventually coming to be 3 km (2 miles) thick.

According to geological theory, approximately two million years ago the land between the Rift Valley and the Mediterranean Sea rose to such an extent that the ocean could no longer flood the area. Thus, the long bay became a lake.

The first such prehistoric lake is named "Lake Gomorrah." Lake Gomorrah was a freshwater or brackish lake that extended at least 80 km (50 miles) south of the current southern end of the Dead Sea and 100 km (60 mi) north, well above the present Hula Depression. As the climate turned more arid, Lake Gomorrah shrank and became saltier. The large, saltwater predecessor of the Dead Sea is called "Lake Lisan."

In prehistoric times great amounts of sediment collected on the floor of Lake Gomorrah. The sediment was heavier than the salt deposits and squeezed the salt deposits upwards into what are now the Lisan Peninsula and Mount Sedom (on the southwest side of the lake). Geologists explain the effect in terms of a bucket of mud into which a large flat stone is placed, forcing the mud to creep up the sides of the pail. When the floor of the Dead Sea dropped further due to tectonic forces the salt mounts of Lisan and Mount Sedom stayed in place as high cliffs. (see salt domes)

From 70,000 to 12,000 years ago the lake level was 100 to 250 m higher than its current level. This lake, called "Lake Lisan", fluctuated dramatically, rising to its highest level around 26,000 years ago, indicating very wet climate in the Near East. Sometime around 10,000 years ago the lake level dropped dramatically, probably to levels even lower than today. During the last several thousand years the lake has fluctuated approximately 400 m with some significant drops and rises.

The Jordan River is the only major stream flowing into Dead Sea. There are no outlet streams.

The northern part of the Dead Sea receives scarcely 100 mm (4 in) of rain a year. The southern section barely 50 mm (2 in). The Dead Sea zone's aridity is due to the rainshadow effect of the Judean Hills. The highlands east of the Dead Sea receive more rainfall than the Dead Sea itself.

The mountains of the western side, the Judean Hills, rise less steeply from the Dead Sea than do the mountains of the eastern side. The mountains of the eastern side are also much higher. Along the southwestern side of the lake is a 210 m (700 ft) tall halite formation called "Mount Sedom".