The first people in Rehoboth and its surroundings are most likely the ǀHūǃgaoben who were a sub clan of the Damaras of the Kalahari. The hot water springs were discovered after the fall of the Damara kingdom during the 16th century, and at this time, the site was named ǀGaoǁnāǀaus, meaning fountain of the falling buffalo. When water was scarce the nomadic Damara people would visit the fountain. Later on, the ǀHūǃgaoben settled in an area about 11km from where Rehoboth is situated in the 1700s. They decided to settle a distance away from the springs of Rehoboth so as to not chase away game roaming site.
In 1845, the ǁKhauǀgôan (Swartbooi) clan arrived with their leaders Willen Swartbooi and Franz Heinrich Kleinschmidt of the German Rhenish Missionary Society. In that very year, Kleinschmidt named the area Rehoboth and established a missionary station there. In the year 1864, the Orlam Afrikaners attacked Rehoboth causing the Nama people to leave the area.