This island lies about 800 m from the mainland, it is located at the, northern entrance of Saldanha Bay in the Benguela current, which is an upwelling system. It is a small island, about 8.300 square kilometers. It is almost rectangular and fairly flat, with the highest point raising about 9 m above sea level. Parts of the island consist of smooth rock and big boulders, though there are patches of shallow soil, guano, sand and shell fragments. Most of the central areas of the island are occupied by nesting Cape Gannets, whereas other nesting seabirds are mostly confined to the periphery. One exception is; the Kelp Gull(Larus Dominicanus) that have managed to establish themselves in the very centre of the island, although in low numbers. The few rocky outcrops in the midst of the gannets' nesting ground are used both by: 'Crowned and Cape Cormorants'.
The scarce vegetation consists mostly of low herbs that grow during the Winter months but there is almost no vegetation during the Summer. There are no terrestrial mammals on Malgas Island. The paucity of the flora and fauna found at Malgas Island can be traced to its history. It can be said that Malgas, as well as all the other coastal islands of Southern Africa, are part of the continental plate. During the Pleistocene Glaciations (12 000 years ago) were part of the mainland. 2000 years ago the sea level was also at least 3 m higher than it is at present. During this time most islands, including Malgas, were either completely covered by water (appearing only at low tide) or were frequently awash by high seas during storms at spring tide. Clearly, most terrestrial flora and fauna was completely eradicated from the islands. The other factor that has a negative effect on the island's biodiversity are the seabirds themselves. The high density of gannets literally covers everything in guano, which, in spite of its famous fertilizing qualities, is in itself quite inert and highly offensive to ones nose!