In chapters 1-3, Porphyry explains that, at a basic level the cave represents the universe. More specifically, the cave is related to earth elements such as stone and rock and therefore represent matter. The water is a related symbol representing the elements that are formed by matter.
At another level, the cave represents both the beauty of the visible world and the obscurity of the invisible world, therfore it can also symbolize every invisible power in general. (''Again, since a cave has a twofold similitude, it must agree in some particulars with sensible substance, but in others with an intelligible essence''.)
Porphyry gives examples such as the use of the cave in Persian initiation rituals of Zoroastrian/Mithraic tradition; Chronos locks up his offspring in a cave; Demeter teaches Persephone in a cave with her nymphs; and Plato's cave allegory, naturally. Because of the water imagery, the cave here is more related to generation and matter. He relates that, in ancient Greece, caves are considered sacred to Naiads.