Approximately 5 mya, the Arava Rift Valley was formed, with rivers changing their courses, carving out the inside of the crater which was a softer rock than that overlying.

This spring serves as the sole natural water source within the crater, supporting a significant portion of its wildlife population, including onagers and ibex.

Giv'at Ga'ash, a black hill in the north of the makhtesh, was once an active volcano which erupted thousands of years ago and caused it to be covered in lava which quickly cooled in the open air, converting it into basalt.

Limestone covered by basalt can also be found in smaller black hills in the southern part of the makhtesh, including Karnei Ramon.

It later rose up through cracks in the Earth's surface, and today stands in striking contrast with the nearby creamy coloured southern wall of the crater, as a black sharp-edged rock.

The pteriidan bivalve Family Ramonalinidae is found in early Middle Triassic rocks of Makhtesh Ramon and was named after this feature.

These ruins acted as a way station for the traders and their animals (khan is the Arabic word for a caravanserai) as they proceeded further westward to the Mediterranean seaport city of Gaza.

Located atop the northern cliff of the crater, one can find Metzad Mahmal, the remnants of a stronghold employed by the Nabataeans and the Romans to safeguard the Incense Route.