Located at the confluence of five ocean currents, the cold Humboldt Current from the South, the cool Peruvian Counter-Current, Cromwell Equatorial Under-Current, the tropical Panama Current and South Equatorial Current conditions in the islands depend on the prevailing current and where the island is relatively located in the current. This mix of water temperatures and nutrient rich upwelling of Antarctic waters gives the Galapagos Islands their unique climate and diverse marine life. The islands volcanic make up also adds to the complexity of the environment. The porous lava provides small fish the protection they would normally receive from coral reefs, which are few in these tropical waters.

Home to a variety of life forms the Ocean consists of a variety of layers. The plants and animals that live within the ocean often exist at a particular level or layer that can be divided into 3 categories. The Benthos is plants including kelp and animals including starfish, which depend on or live on the bottom. The Nekton is swimming animals including fish and whales, which move independently of the current. The current carries the Plankton, which consists of various microscopic creatures,.

Benthic plants and animals live in particular regions within the ocean. The cold region between the shoreline and continental shelf is home to sponges, crustaceans, attached algae and polyaete worms. The deepest parts of the ocean beginning at the continental slope and extending to the ocean floor make up the benthic zone. This region is sparsely populated with filter feeders and deposit feeders such as sea spiders and sea lilies.

Nekton fish are generally found swimming freely in the warmer well-lit waters above the continental shelf. In the darker regions beginning at the continental shelf giant squid can be found.

Plankton is the most prevalent life and food source in the ocean. Phytoplankton, which carries on photosynthesis near the ocean surface, serves as food for the zooplankton and fish.

The low ratio of surface water to deep water and the lack of seasonal nutritional enrichment cause most of the ocean to be a watery desert especially in the tropics. The most abundant life occurs in areas of upwelling and in the Arctic and Antarctic waters.

In the case of Galapagos the abundant life occurs due to an upwelling of Antarctic waters. As deep waters enter the Antarctic they are frozen becoming saltier and denser. This denser water sinks and together with the surface water moves north from the continental plate. The water is replaced by nutrient rich southward moving water between the surface and bottom layers. That southern moving water with its rich nutrients rises to the surface stimulates the growth of phytoplankton. The phytoplankton is consumed by zooplankton and other krill, which in turn are consumed by fish and whales.

As these rich Antarctic waters are pulled away from the shore they become the Antarctic Circumpolar Current. At the tip of South America part of this current is broken off forming the Humboldt Current. The Humboldt Current continues up the coast of South America and reaches the Galapagos Islands from June to November.

The Earth's rotation and strong seasonal winds push the surface water away from the western coast of South America and the islands.  Upwelling of the nutrient rich water occurs on the western edge of the continental shelf replacing the warmer waters. The abundant marine life within the Galapagos Archipelago thrives in these nutrient rich waters.

In years where the "El Niño Current" occurs the cold waters from the Antarctic do not reach the islands and due to the lack of upwelling the food chain is broken. This break affects many sea birds including the flightless cormorants, Galapagos penguins & animals including the marine iguanas.