The lagoon, lying mostly to the northwest of the islands is relatively shallow, the greater part of it lying at depths between 8 and 18m. Lithified Pleistocene calcarenite deposits submerged beneath the lagoon provide a relict topography which seems to be a dominant factor controlling the broad features of lagoonal bathymetry. For instance: (1) North Rock is an exposed remanent of a Pleistocene aeolianite which presumably extends along the line of the Ledge Flats reefs; (2) Many of the reefs (Three Hills Shoals, Baileys Bay Flats) lie on crescent lineations reminiscent of the aeolianite hills of Bermuda itself; (3) Aeolianite has been reported as the base for the south shore boilers.

Within the lagoon, literally thousands of reefs rise up to within a few meters of sea level. They are of many different types, including fringing reefs near the shore, small knobs where the lagoon flow is shallow, cellular reefs especially at the inner margin of the Ledge Flats, and pinnacle and mesa-like forms rising from the deep parts of the lagoon floor.