Within the confines of the Botanical Garden are ancient burial caves from the Second Temple period. One of the more well known burial caves is the Nicanor Tomb, consisting of limestone ossuaries and a revealing inscription written in Hebrew and Greek: "The bones of Nicanor of Alexandria who made the doors Nicanor Alexa." Archaeologists surmised that the tomb contains the hidden remains of Nicanor of Alexandria, a Jewish benefactor who provided the two copper gates for the Second Temple. Today, visitors can see reconstructed ossuaries within the burial caves, as the originals have been moved for display to the British Museum in London.

The Babylonian Talmud, Tractate Yoma 38A, relates a miraculous story regarding Nicanor:

"Miracles happened to Nicanor's doors. The sages recount what were the miracles of his doors: When Nicanor was returning from Alexandria in Egypt to bring the doors a huge wave threatened to engulf him. Thereupon, he took one of the doors and cast it into the sea, but still the sea continued to rage. When they prepared to cast the other one into the sea, Nicanor rose and clung to it, saying, 'Cast me in with it.' The sea immediately became calm. He was, however, deeply grieved about the other door. As they reached the harbor of Acre (present-day Acco in Israel), the door broke the surface and appeared from under the sides of the boat."

The archaeological site is also noteworthy for the Nazir caves, used as a family burial ground for the Nazir family of the first century CE. Inside the tomb, two burial caskets and fourteen ossuaries were found, most of which were adorned. Some of them had Aramaic inscriptions recounting Hanania Bar-Jonathan the Nazir, his wife Shalom and other family members.