Local Maori legends explained the boulders as vegetables (gourds, kumaras and calabashes) washed ashore from the large sailing canoe Arai-te-uru when it was wrecked upon landfall in New Zealand hundreds of years ago. This legend tells of the rocky shoals that extend seaward from Shag Point as being the petrified hull of this wreck and a nearby rocky promontory as being the body of the canoe's captain. This fits well with other Maori legends telling that everything was gigantic in those ancient ages.

Scientists explain the Moeraki boulders as septarian concretions, were formed in ancient sea floor sediments. They were created by a process similar to the formation of oyster pearls, where layers of material cover a central nucleus or core. For the oyster, this core is an irritating grain of sand. For the boulders, it was a fossil shell, bone fragment, or piece of wood. Lime minerals in the sea accumulated on the core over time, and the concretion grew into perfectly spherical shapes up to three metres in diameter. The original mudstone seabed has since been uplifted to form coastal cliffs. Erosion of the cliffs has released the three tonne captive boulders, which now lie in a haphazard jumble across the beach. Further erosion in the atmosphere has exposed a network of veins, which gives the boulders the appearance of turtle shells.

The Moeraki Boulders are located on Koekohe Beach between Moeraki and Hampden, about 75 km north of Dunedin and about 40 km south of Oamaru and accessible by Moeraki Boulders Road followed by a short walk along the beach. You will also find the Moeraki Boulders Cafe, Bar and Gift Shop. Access to the beach from the visitor centre costs $2 per person. You can also drive about 300m south from the main road and use the free public carpark and free access to the beach.

Similar boulders can be found at Shag Point, and the nearby swimming beach of Katiki. Also very similar boulders, which are as much as three metres in diameter and called "Koutu Boulders", lying on the beach between Koutu and Kauwhare points along the south shore of the Hokianga Harbour of Hokianga, North Island, New Zealand. In Hawke's Bay in the North Island, scientists have found that the central core of similar boulders contained perfectly preserved skeletons of turtles, sea snails and extinct reptiles, such as plesiosaurs.