[1]: 354 Water currents around the reef tend to originate from the southeast, propelled by trade winds.
[7] The reef is quite large compared to its neighbours, stretching 40 kilometres (25 mi) north to south.
[5] : 2206 Rising up from water over 1 kilometre (1 mi) deep, most of the reef lies at a depth of just 1–4 metres (3–13 ft).
[1]: 353 The reef is part of the Coral Sea Marine Park, and is designated as an IUCN protected habitat or species management area.
Concentrations of sponges can reach 1.2 kilograms (2.6 lb) per 1 square metre (11 sq ft), and they cover around 7.3 per cent of the reef flat.
[4]: 184 At least one of these species may be phototropic,[4]: 183 and through partnership with symbiotic cyanobacteria these sponges may extract over 50 per cent of their nutrition from sunlight.
[4]: 184–185 Due to its isolation from local human influence, Flinders Reef is a candidate for the location of a Global Boundary Stratotype Section and Point to mark the beginning of the Anthropocene.
[2] The transition to the Anthropocene can be seen in samples of Porites coral, which can live for hundreds of years and continue growing throughout this period.