Endless Ocean is the third installment in the Everblue series, which explores underwater worlds. The game focuses on exploring the game world and cataloguing the various species of animals found there. Unlike its predecessors, Endless Ocean differs from them in that the traditional "game elements" are mostly gone - whereas Everblue 2 set a goal for the player by having them search for treasure underwater, Endless Ocean lets the player explore at their own pace. The player is not obligated to search for these items in order to progress through Endless Ocean as the game is mostly freeform exploration with no overarching plot.
The full game world is only accessible in parts at a time, as opposed to the similar Aquanaut's Holiday. Players can freely move their boat around a map of the entire game world on which diving tours are limited. In this way, the player can choose for themselves which areas of the game world to access without having to endure loading times; however, moving from one play area to another requires returning to the boat and using the map.
Each animal species is tracked in three levels of detail - no information, three small pieces of information, and three large pieces of information. Fish, dolphins, whales, and sea lions are the most common animals, but penguins and pelicans are also included. During the first few hours of gameplay, the player unlocks a variety of extra features, including night diving, underwater cameras, and aquariums they can populate with animals they've encountered.
It also adds online multiplayer to the series, allowing players to dive together using Nintendo's Wi-Fi Connect service. Rather than using the Wii system's built-in friend code, the game generates its own, requiring the player to keep a separate friend list.