In EcoQuest: The Search for Cetus, the player is cast into the role of Adam, the twelve-year-old son of the famous ecologist Noah Greene. One day, his father rescues a dolphin from an abandoned fish net. As Adam becomes more friendly with the creature, he is amazed to discover that the dolphin can talk! Adam finds out that his new friend is Delphineus, the messenger of the whale king Cetus. As a qualified scuba diver, Adam is chosen to venture into the underwater kingdom of animals known as Eluria, and help its inhabitants.

The game's interface and basic gameplay are similar to those of other Sierra adventures: the player interacts with the environment by selecting icons that represent verb commands ("Look", "Talk", "Use", etc.) and applying them to objects or characters. Compared to most other adventure games by the same company, the difficulty level is lower, with the intention of making the game more suitable for younger players; for instance, it is impossible to "die" or get irrevocably stuck in the game.

Despite its supernatural elements, EcoQuest contains educational material. The inhabitants of the deep see are realistically depicted, and there is plenty of information concerning their life habits, environment, and the threats posed to them by human beings.