The protected area is given its name by the Barreiro da Faneca, nicknamed the "Red Desert of the Azores", an arid and clayey landscape formed during the Pliocene, unique not only to the island but to all of Portugal.

These clays were initially basalts formed during the Pliocene (approximately 3-4 million years ago) which were then covered by a layer of pyroclasts as a result of an essentially explosive eruption.

Due to the hot and humid climate present during that epoch, the basalts were intensely altered and eroded, originating the current reddish clays and the associated semi-desert-like landscape.

[2] The biome of the landscape has changed a lot since its formation, with its characteristic barren terrain becoming progressively smaller as native plants gain territory.

[2][4] The group of bays are limited by large cliffs with extreme slopes, with altitudes ranging from 50 to 150 metres (160 to 490 ft) above sea level, and are recognized for their ecological importance and distinct landscapes, that include the islet of Lagoinhas, known for support of marine bird habits and populations of migratory and marine birds like Shearwaters (Calonectris borealis) and terns (Sterna hirundo and Sterna dougallii).