Geologically, it is formed of sedimentary rock and is situated on the transition zone between the relatively shallow and brackish waters of the gulf and the deeper marine waters of the open ocean.

Though currently uninhabited, it contains archaeological remains and is sacred to the inhabitants of nearby Puná Island.

The level of marine biomass productivity around the island is among the highest on the Ecuadorian coast.

Santa Clara has been designated an Important Bird Area (IBA) by BirdLife International because it supports colonies of seabirds, including brown pelicans, magnificent frigatebirds and blue-footed boobies.

The fauna of the surrounding waters includes 58 species of fish, olive ridley sea turtles, humpback whales, common bottlenose dolphins and South American sea lions.