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The wreck site of BATAVIA lies in four to seven meters of water on the south-west corner of Morning Reef, off Beacon Island, in the Wallabi Group of the Houtman Abrolhos 80 kilometres off the coast from Geraldton in Western Australia. The main body of the wreckage lay in a shallow depression in the reef approximately 50 meters long and 15 meters wide. A thin hard crust of dead coral, held together by live coral overlay a loosely packed deposit of sand and coralline rubble which protected the remains of the BATAVIA's hull and cargo.

The wrecksite of the BATAVIA, its relics and its associated land sites are protected under the Historic Shipwrecks Act (1976).