During the slight delay between closing the mouth and opening the gill flaps, plankton is trapped against the dermal denticles which line its gill plates and pharynx. This fine sieve-like apparatus, which is a unique modification of the gill rakers, prevents the passage of anything but fluid out through the gills (anything above 2 to 3 mm in diameter is trapped). Any material caught in the filter between the gill bars is swallowed. Whale sharks have been observed "coughing" and it is presumed that this is a method of clearing a build up of food particles in the gill rakers.

Whale sharks congregate at reefs off the Belizean Caribbean coast, supplementing their ordinary diet by feeding on the spawn of giant cubera snappers, which spawn in these waters between the full and new moons of March through September.