Pandora has a linear un-vegetated shingle cay which towards the west is relatively low, rising only 1.5m above the reef flat. At its eastern end the ridge heightens as it curves around a shallow pool and reaches a height of more than 3m, remaining above all except the highest tides.

The waters around Pandora Reef are often turbid and photographic quality at the sites is influenced by water clarity. Extensive areas of coral bleaching occurred during the summer of 1992 associated with elevated sea temperatures and flood plumes produced by Cyclone Sadie. In January 1998 there was moderate bleaching of hard and soft corals. Four weeks later a major flood event in the Townsville region caused further bleaching which was reported to effect around 80% of the corals on Pandora Reef to a depth of 10m (DeVantier, Fabricius pers comm).

The 4 sites each consist of a single line. Pandora 1 and 2 are at the front of the reef in about 4m and 10m of water. Pandora 3 and 4 are at the back of the reef and both of these lines have a bend in them.