According to the ancient Greek historian Herodotus, human presence in the cave dated back to 3000 BC but excavations carried out by the Municipality of Marmaris in 2007 pushed this back by almost 12,000 years.

Research conducted in the cave revealed the existence of a cult of the Mother Goddess Leto, the mother of God Apollo and Goddess Artemis, in the ancient city of Physkos. Worship took place around the main rock which is surrounded by stone altars in a semi-circle raised about 30 cm from the ground.

Offerings in the form of cremations, glass beads, terracotta, and sculptures of Leto were placed on these elevated stones.

The cave was also used during the Roman period.

Nimara Cave was declared a protected area in 1999. It shelters trogloxene butterflies, identical to those living in Fethiye‘s Butterfly Valley.

The Marmaris peninsula is the westernmost habitat for Tulipa armena, which normally grows in Eastern Turkey, Iran, and Transcaucasia at much higher altitudes.

The plants may have been introduced during the Ottoman period.