Endless Ocean places the player in the shoes of a scuba diver exploring the fictional Manaurai Sea in search of sea life and sunken treasure.Here, they will encounter a number of marine species ranging from smaller fish and penguins to massive whale sharks, manta rays and humpback whales.The range of marine wildlife in the game is very extensive and includes many common and also less common species. The player will also encounter a dolphin that can become a companion on dives. Dangerous creatures such as sharks will also be evident; however, they pose no threat to the player. The player also has access to a large aquarium habitat that, once available, they can populate with species they have identified.

The game is controlled solely using the Wii Remote, with the player using an on-screen cursor to guide their diver. The game will also feature Wi-Fi play over the Nintendo Wi-Fi Connection service, allowing for several players to dive together.

Arika, the game's developer, previously released the games Everblue and Everblue 2 for the Playstation 2. Both titles featured very similar gameplay to that of Endless Ocean, revolving heavily around scuba diving in search of underwater treasure, as well as photography. The Everblue titles however, are both played from a first person perspective, while Endless Ocean utilizes both a third-person perspective and, by pressing the "2"-Button, the first person perspective for free movement.

Additionally a fixed first person perspective is used for narrow examination.