[11] The remains of the Iron Age settlement at Ein Gedi are located at a tell on the north bank of Wadi Arugot, known in Arabic as Tell el-Jurn (grid position 187/097 PAL) and in Hebrew as Tel Goren.

[citation needed] In Joshua 15:62, Ein Gedi is enumerated among the wilderness cities of the Tribe of Judah in the desert of Betharaba, and in Ezekiel 47:10, it is prophesied that one day, its coastal location will make it into a fishing village, after the water of the Dead Sea has been made sweet: Fleeing from King Saul, David hides in the strongholds at Ein Gedi (1 Samuel 23:29 and 24:1–2) and Saul seeks him "even upon the most craggy rocks, which are accessible only to wild goats" (1 Samuel 24:2).

[citation needed] According to Jewish-Roman historian Josephus, Ein Gedi served as the capital of a toparchy, and there were excellent palm trees and balsam growing there.

[15] During the First Jewish-Roman War, the Sicarii, who fought the Romans until their defeat and mass suicide at Masada, plundered local villages including Ein Gedi.

[16][17][18] Pliny claims that Ein Gedi was destroyed during the war, although the Babatha archive shows that Jews lived there once again during the reign of Hadrian and probably earlier.

The Babatha archive mentions Ein Gedi as a crown property; the Cohors I Milliaria Thracum is attested there, indicating the presence of Roman soldiers there at the time.

According to the archaeologists who excavated the synagogue, the village was destroyed during the early 6th century by Byzantine emperor Justinian as part of his persecution campaign against Jews in his empire.

[20] In April 1848, Lieutenant William Francis Lynch led an American expedition down the Jordan River into the Dead Sea, that stopped at Ein Gedi (Ain Jidy).

[21] In 1998–99, the archaeological expedition of Yizhar Hirschfeld at Ein Gedi systematically excavated what has been called "the Essenes site", first discovered by Yohanan Aharoni in 1956.

It offers various tourist attractions and takes advantage of the local weather patterns and the abundance of natural water to cultivate out-of-season produce.

[23] The kibbutz is also home to the Ein Gedi Eco Park, which functions as both a zoo and an environmental education center, demonstrating sustainable technologies such as solar cookers, greywater systems, mud buildings, and compost toilets.

The Late Roman- and Byzantine-period synagogue and the village remains around it is run as a separate, archaeological park, distinct from the nature reserve and the antiquities contained therein.

The vegetation includes plants and trees from the tropical, desert, Mediterranean, and steppian regions, such as Sodom apple, acacia, jujube, and poplar.

The sinkholes form as a result of the receding shoreline (with the surface of the Sea having shrunk by about 33 per cent since the 1960s), where a thick layer of underground salt is left behind.