The Lagoon is the first area visited in Endless Ocean. It is in the Manaurai Sea. It is comparable to Adventures of the Deep's Atoll Gate. This is where you, as the player, are introduced to the basic mechanics of the game, like turning, swimming, and autoswim.

The Lagoon is home to a multitude of small sea life, like Blue Tang, Moorish Idols, Longnose Butterflyfish, Emperor Angelfish, and Yellow Tang, among others. However, the Lagoon is also inhabited by bigger fish, like the resident Manta Ray that lives there during the daytime. During the night, however, the Manta Ray is gone, and in its place are a Longtooth Grouper, an Ocean Sunfish, and two Green Sea Turtles.

The only treasure located in the Lagoon is a single part of the Pirate's Compass.