St Paul's Islands lie approximately 80 metres off the North-Eastern coast of Malta and are made up of upper coralline limestone (Tal-Pitkal member). The western part of the islands supports a typical maritime garigue community dominated by the golden samphire (Inula crithmoides) and the Maltese fleabane (Chiliadenus bocconei), accompanied by a variety of other species including the sea-carrot (Daucus rupestris) and the eastern phagnalon (Phagnalon graecum subsp. ginzbergeri). Further inwards, the garigue communities also support the Maltese sea-lavender (Limonium melitensis), the cage thistle (Atractylis cancellata), the Maltese toadflax (Linaria pseudolaxiflora), the cretan pellitory (Parietaria cretica) and the Maltese dwarf garlic (Allium lojaconoi).

The eastern section of these islets is highly exposed and the vegetation in this area, which is dominated by three maritime species (Inula crithmoides, Limonium melitensis and Arthrocnemum macrostachyum), is restricted to areas around small boulders and to crevices, cracks and temporary rockpools. The central part of the eastern section is more sheltered from wind and sea spray and supports the highest diversity.

St Paul's Islands support an endemic race of the Maltese Wall Lizard (Podarcis filfolensis kieselbachi) and a population of the terrestrial snail Trochoidea spratti, occurring on the islet under the form schembrii.

Mepa scheduled St Paul's Islands as a Level 1 Site of Scientific Importance and a Level 1 Area of Ecological Importance as per Government Notice No. 827/02 in the Government Gazette dated September 20, 2002.