Due to the geology of the chalk, wave action by the sea has created over 200 sea caves. The diversity and large numbers of caves at Flamborough Head are associated with faulting and jointing in the sea cliffs. The sea caves are restricted to the north and east sides of the Headland due to the chalk being harder and more exposed to wave action than the softer chalk on the south side.
The chalk bedrock not only allows marine plants and animals to attach to it but because it is relatively soft, specialist organisms are able to burrow into it. The chalk sea caves are internationally important for their specialist lichen and chalk boring micro-algal species.
Some of the caves are only partly submerged whilst others are completely submerged by the action of the tides. The sea caves at the eastern end of the Headland are noted for being rich in certain sublittoral (underwater) species including the chalk boring yellow sponge Cliona celata.
The sea caves provide shelter to a variety of larger marine animals on occasion, such as Common and Grey Seal as well as breeding seabirds such as kittiwake and shag.