While forming a distinct geographic region, the Mediterranean Sea is biogeographically not considered a separate entity from the adjoining North Atlantic Province since the Straits of Gibraltar is not apparently an important biogeographical barrier. Generally, the fauna and flora of the Mediterranean are made up of a large number of North Atlantic forms and a rather large ptoportion of endemic forms. Thereare only minor contributions from other regions. The Mediterranean subprovince may itself be divided into four main biogeographical regions, including the Alboran Sea, the Western Basin, the Adriatic Sea and the Eastern Basin, which in turn are divided into various subregions. The biogeographic position of the Maltese Islands seem to place these in the Central Mediterranean where several different Mediterranean biogeographical regions meet. Because of the continuous circulation of sea water at the Straits of Gibraltar, the surface temperature and salinities in the Mediterranean are variable varying between 12.7-14.5^oC and 38.4-39.0 parts per thousand respectively. The values for Maltese waters vary between 15-26^oC and 37-38 parts per thousand respectively. The continuous water flow at the Straits also result in an outflow of nutrients out into the Atlantic Ocean. This causes the Mediterranean Sea to be one of the poorest seas known. Maltese waters are no exception.

The Mediterranean coastal environment may be divided into several zones. The uppermost region is the Supralittoral Zone which is permanently exposed to the air but is kept wet by sea-spray and high waves. The second zone is the Mediolittoral Zone which is regularly exposed and submerged through wave action. The third zone is the Infralittoral Zone which extends to a depth of about 30-40 m depending to the extent of light penetration. This zone is followed by the Circalittoral Zone which extends to about 200 m and represents the maximum depth at which plant life of any sort can live. These four zones make up the Littoral System. Beyond this depth starts the Deep System which in the Mediterranean is made up of the Bathyal Zone (200-3000 m) and the Abyssal Zone (3000-6500 m). The Hadal Zone (>6500 m) is not represented in the Mediterranean. The Littoral System zones can vary according to whether the substratum consists of hard rock or soft sand or mud. Each substratum or zone type houses typical flora and faunal assemblages which vary from one locality to another.