Endless Ocean is the third installment in the Everblue series, games focused on exploring an underwater world. The main focus of the game is exploration of the game world and cataloguing the various species of animals found there. Endless Ocean slightly differs from its predecessors in that the traditional "game elements" have been mostly removed - where Everblue 2 set a goal for the player by having them search for treasure underwater, Endless Ocean is more freeform and just lets the player explore at their own pace. There are still treasures to find, but as Endless Ocean is mostly freeform exploration and has no overarching plot, the player is in no obligation to look for these items to progress through the game.

Unlike in the similar Aquanaut's Holiday, only a small area of the full game world is seamlessly accessible at any one time. Diving tours are limited to a certain area around the player's boat, which can be freely moved about a map of the whole game world. This allows the player to choose for themselves the area of the game world they can access without having to bear loading times; however it is not possible to move from one play area to another without returning to the boat and using the map to move it around.

The game keeps track of the species of animals encountered and examined in three levels of detail - no information and three small pieces of information on each species. The animals are mostly marine life - fish, dolphins, whales, sea lions - but also include various coastal and marine birds, such as penguins and pelicans. There are a number of extra features that unlock during the first few hours of gameplay, including night diving, an underwater camera/photo album and an aquarium the player can populate with species of animals they've encountered in the open sea.

This title also adds online multiplayer to the series, allowing for players to use Nintendo's WFC service to go diving together. The game does not use the Wii system's built-in friend code but instead generates its own, requiring players to keep a separate friend list for the game.