This species is commonly found in shallow waters on and near coral reefs and occasionally in brackish waters. Juveniles are typically found in extremely shallow water (±15 to 100 cm) inside lagoons, often swimming along the shoreline; adults typically occur on shallow parts of the forereef, often moving over the reef crest and onto the reef flat at flood tide. Individual adults inhabit a relatively small home range of ±2.5 km2 and appear to reside close to their home reef but occasionally cross deepwater channels between adjacent reefs.

They are also found in mangrove areas, moving in and out with the tide and even in fresh water near the sea. They occur singly or in small groups. Adults often aggregate in reef channels at low tide. This is one of the three most common reef sharks in the Indo-Pacific, the two others are the grey reef shark, Carcharhinus amblyrhynchos and whitetip reef shark, Triaenodon obesus.

On the infrequent occasions when they swim in oceanic waters, grey reef sharks often associate with marine mammals or large pelagic fishes, such as sailfish (Istiophorus platypterus). There is an account of around 25 grey reef sharks following a large pod of bottlenose dolphins (Tursiops sp.), along with 25 silky sharks (C. falciformis) and a single silvertip shark.[13] Rainbow runners (Elagatis bipinnulata) have been observed rubbing against grey reef sharks, using the sharks' rough skin to scrape off parasites.[14]

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There is a variety of biotic reef types, including oyster reefs and sponge reefs, but the most massive and widely distributed are tropical coral reefs. Although corals are major contributors to the framework and bulk material comprising a coral reef; the organisms most responsible for reef growth against the constant assault from ocean waves are calcareous algae, especially, although not entirely, coralline algae.
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