The beach stones, pebbles and gravel accumulating between the wooden breakwaters along the Whitstable shoreline in Kent, are mostly flint with white chalk stones and brownish phosphatic nodules.
Lots of the beach stones have holes in them of various sizes and shapes and originating in different ways. Some stones have more than one type of hole in them. Sometimes with the flint pebbles there are very ancient holes made by the wearing away of softer inclusions including trace fossils and fossils that were embedded in the silica. See the thread on the Natural History Museum Nature Plus Forum.
For explanations and other examples of stones with holes in them that result from the activities of seashore creatures like burrowing bivalve molluscs, infesting marine worms, and sponges have a look at lots of previous posts on Jessica’s Nature Blog about pebbles with holes.