Each of the reefs rises steeply from the seabed below. Much of the reef area dries at low tide, but besides Sandy Islet of Scott Reef South, there are only a few rocks and sandbanks above the high water mark.
Scott Reef South is a large crescent-shaped formation that has a rare and unusual double reef crest. Its lagoon, has depths of over throughout the greater portion. The reef with its lagoon covers an area of.
Scott Reef Central, because of its proximity occasionally subsumed within Scott Reef South, lies off West Hook, with Sandy Islet at . This reef falls dry to the extent of from the islet. There is a conspicuous tower on the islet and also a boulder with a height 2.4 m near its northern end. A detached reef, which dries, lies northeast of Sandy Islet. The passage between Scott Reef South and Scott Reef Central is only deep, much less than the passages between the other reefs.
Scott Reef North consists of a large, approximately circular-shaped, reef lying southwest of Seringapatam Reef. The reef is composed of a narrow reef-crest that is backed by broad reef flats – much of which becomes exposed at low tide – and a deep central lagoon that is connected to the open sea by two delta-like channels. The reef with its lagoon covers an area of.
Seringapatam Reef is located at, north of Scott Reef North. It is an egg-shaped reef, with a total area of approximately, which is about evenly divided between lagoon and reef flat. Its narrow reef rim encloses a relatively deep lagoon. Much of the reef becomes exposed at low tide. There are large boulders around its edges, with a few sandbanks, which rise about above the water, on the west side. Seringapatam Reef covers an area of . Captain Edwin Courtenay of was on a whaling voyage when he discovered the reef on 23 August 1839. He named the reef for his ship.
Scott Reef was extensively affected by coral bleaching in 2016, which killed approximately 80% of corals. This followed a previous extensive coral bleaching in 1998 during which "up to 80 per cent of Scott Reef corals died" but from which the reef did recover in the subsequent 10–15 years. Heat stress was the highest ever recorded in 2016. Nevertheless, given continuing and measurable climate change and the "direct correlation between increased temperatures and coral bleaching", the consequent increasing frequency of coral bleaching warrants concern that Scott Reef may not recover and survive from the 2016 bleaching event.
