The ocean is another world. Beneath the surface of the sea, all the sounds and the stress of society are muffled away to nothing. In Aquanaut's Holiday, the player takes the role of a renowned oceanographer has been pushed to the limit by the constant attention of the press, environmentalists, and the government. It's time to leave it all behind, on an open-ended mission to explore one of the last unmapped areas in the ocean and create a new coral reef there.

The game is played entirely at the player's pace. The only real goals and time limits are those that the player sets. The main point of the experience is simply to explore the virtual undersea environments. The game provides several ways in which to interact with the wildlife, and information gained from the local sea creatures can provide clues toward how to design a better coral reef. There are shipwrecks and ruins to discover, dozens of species of fish and sea life to observe, and no reasons to hurry.