Komodo is one of the long arc of islands running from Sumatra towards Irian Jaya along the line of a tectonic subduction between the Sunda and Sahul shelfs. It is the largest (34,000 ha) of a small archipelago between the larger islands of Sambawa and Flores. The topography is generally steep and rugged owing to its volcanic origin and is dominated by a range of rounded north-south oriented hills between 500-600m high. Relief is steepest to the north-east, notably in the peak of Gunung (Mount) Toda Klea which is precipitous and crowned by deep, rocky dry gullies. The coastline is irregular with little flat ground, numerous bays, beaches and inlets separated by headlands, often with sheer cliffs falling vertically into the sea. To the east, across the Lantah Strait, Padar is a small, narrow island which rises steeply from surrounding plains to 200-300m. Further east, the second largest island in the Park, Rinca (20,000 ha), is separated from Flores by a very narrow strait. Gili Motong is a much smaller island to its south-east.
The topography of the southern part of Rinca is dominated by the Doro Ora massif (667m); to the north the steep-sided peaks of Gunung Tumbah and Doro Raja are 187m and 351m respectively. As with Komodo and Padar, the coastline is rugged and rocky although sandy beaches are found in sheltered semi-enclosed bays. The mainland sections of the Park, Mbeliling – Ngorang forest and Way Wuul Mburak Park, lie on the rugged coast of north-western Flores where surface fresh water is more abundant than on the other islands. The islands were probably formed by vulcanism in the Eocene era though the west side of Komodo preserves Jurassic rocks. Deposits are generally resistant volcanics, volcanic ash, conglomerates and coral formations raised by tectonic movement. There are frequent tremors though no active volcanoes. The soils are rocky and shallow (Sumardja,1981; PHKA, 2004).
The seas around the islands are among the most productive in the world due to upwelling and a high degree of oxygenation resulting from the strong tidal currents which flow through the Sape Straits to the west (Kvalvagnaes & Halim,1979). The marine site has sea mounts, semi-enclosed bays and seagrass beds north of Rinca Island. Fringing and patch coral reefs are extensive and best developed in the west- and north-facing areas, the most intact being on the north-east coast of Komodo and the south-west coasts of Rinca and Padar.