The Alboran domain, the seafloor beneath the Alboran Sea (known as the internal zones) together with the surrounding mountains (known as the external zones; the Gibraltar Arc and Atlas Mountains), is mostly made of continental crust and marks the westernmost terminus of the terranes that were subducted between the African and Eurasian Plates when the Tethys Ocean closed.

Reoccurring earthquakes at a depth of about 600 km (370 mi) indicate that this subduction is ongoing and that complex interactions between the lithosphere and mantle are forming the region.

In 2003, the World Wildlife Fund raised concerns about the widespread drift net fishing endangering populations of dolphins, turtles, as well as other marine animals.

In 2023, the European Union, Morocco, and Algeria agreed to ban bottom fishing practices around Cabliers Bank, protecting the only cold-water coral reef known to be growing in the Mediterranean.

The moderating influence of the Atlantic has allowed many relict species in the Baetic and Rif mountains to survive the climatic fluctuations of the last few million years that have caused them to become extinct elsewhere around the Mediterranean basin.