The objective of this study was to determine at what level the shell mineralization of Anodonta cygnea, a shallow freshwater bivalve, is influenced by external physical—chemical factors, mainly concerning the habit and microstructure of the calcium carbonate crystals. A detailed examination of the inner shell layers of A. cygnea was carried out by scanning electron microscopy in animals living under natural environment conditions and after being exposed to artificially high hydrostatic pressure. Groups of 6 animals were exposed to different hydrostatic pressure (10, 20, 40, or 80 bar) in a hyperbaric chamber for 10 days. In general, we noted that the high pressure induced strong changes in the microstructure of all regions of the shell inner layer in A. cygnea, probably by altering organic matrix deposition, under every hyperbaric value. In fact, observations of the prismatic layer showed some significant alterations, presenting fibrous spherulitic crystalline arrangements instead of the nondenticular composite crystals. At the beginning of the nacreous layer, experimental animals showed several (5–7) superimposed lamellae consisting of unconnected round tablets. In the following regions, the nacreous layer with hexagonal-rhombohedral crystals displayed an intense growth resembling columnar formations resulting from a greater number of mineral layers, many more than would be expected. A similar phenomenon was also revealed in the inner palliai line regions of the exposed A. cygnea bivalves, with simultaneous visualization of more than 10–15 layers of nacre in contrast with 3–4 seen in natural situations. Curiously, similarly altered microstructures were observed in shell calcareous layers of a hydrothermal vent deepsea bivalve Bathymodiolus azoricus, particularly in the nacreous layer. This natural occurrence, together with the experimental work on A. cygnea, might imply that hydrostatic pressure is a physical parameter of great importance in microstructure definition. The basic mechanism is probably related to deficient chitin (or similar) polymerization, which promotes the vertical growth of the nacre crystals.