The lagoons of seven French Polynesia and Cook Islands pearl farming atolls (Raroia, Takume, Mopelia, Takapoto, Ahe, Takaroa and Manihiki) were surveyed using multibeam and mono-beam sounders. From the detailed bathymetry, morphometric variables (average and maximum depth, frequency-area of depth, lagoon area and volume) are computed and compared. Remarkable geomorphological structures highlighted by bathymetric variations include deep reticulated structures and pinnacles. The seven atolls appear very different in abundance, size and density of these entities. Considering them as markers of the geological, sedimentological and eustatic processes that shape atoll lagoons, they are discussed in the context of the general theory of atoll lagoon formations involving karstic dissolution during Pleistocene or earlier low sea-level stands. In terms of pearl farming management, accurate bathymetric maps help pearl oyster wild stock assessment, development of circulation and biogeochemical models, better lagoon zoning and strategy to remove pearl farming derelict gears.