Only the three largest islands – Malta (Malta), Gozo (Għawdex), and Comino (Kemmuna) – are inhabited. The smaller islands (see below) are uninhabited. The islands of the archipelago were formed from the high points of a land bridge between Sicily and North Africa that became isolated as sea levels rose after the last Ice Age. The archipelago lies on the edge of the African tectonic plate where it meets the Eurasian plate.

Numerous bays along the indented coastline of the islands provide good harbours. The landscape consists of low hills with terraced fields. The highest point in Malta is Ta' Dmejrek, at 253 m (830 ft), near Dingli. Although there are some small rivers at times of high rainfall, there are no permanent rivers or lakes on Malta. However, some watercourses have fresh water running all year round at Baħrija, l-Imtaħleb and San Martin, and at Lunzjata Valley in Gozo.

Phytogeographically, Malta belongs to the Liguro-Tyrrhenian province of the Mediterranean Region within the Boreal Kingdom. According to the WWF, the territory of Malta belongs to the ecoregion of "Mediterranean Forests, Woodlands and Scrub".

The minor islands that form part of the archipelago are uninhabited and include:

Barbaganni Rock (Gozo)
Cominotto, (Kemmunett)
Delimara Island (Marsaxlokk)
Filfla (Żurrieq)/(Siġġiewi)
Fessej Rock
Fungus Rock, (Il-Ġebla tal-Ġeneral) (Gozo)
Għallis Rock (Naxxar)
Ħalfa Rock (Gozo)
Large Blue Lagoon Rocks (Comino)
Islands of St. Paul/Selmunett Island (Mellieħa)
Manoel Island, which connects to the town of Gżira, on the mainland, via a bridge
Mistra Rocks (San Pawl il-Baħar)
Taċ-Ċawl Rock (Gozo)
Qawra Point/Ta` Fraben Island (San Pawl il-Baħar)
Small Blue Lagoon Rocks (Comino)
Sala Rock (Żabbar)
Xrobb l-Għaġin Rock (Marsaxlokk)
Ta'that il-Mazz Rock