Fishdom H2O: Hidden Odyssey revolves around the story of an animal rights activist and her quest to find her missing brother. You play the role of Marina, an animal rights activist who becomes interested in learning more about Celine, a killer fish that has just been stolen from a cove. Celine, though thought to be a lover of animals, has been involved in the illegal trade of endangered animals in the past. As Marina begins investigating the theft, she comes across a series of coordinates leading her into a secret cove. There, she finds a strange manor known as Fishdom H2O: Hidden Odyssey, where some powerful creatures are experimenting on captured fish.
Once you've started playing, you'll notice that most of the scenes are taken from the underwater world of Fishdom H2O: Hidden Odyssey. For example, one scene involves a diver searching through the ocean floor using sonar to locate a large lump that resembles a head. The player must guide this sonar anchor down to the exact location where the anchor will fall, while avoiding obstacles in the way such as sharks. Once the platform drops, the screen will shift to show another underwater scene in which Marina uses a diving bell to search for Celine.
In order to progress through the game, you'll need to make use of a variety of tools such as the fishing pole, a camera, and a map. You can also purchase special fish in Fishdom H2O: Hidden Odyssey that can be dived up to the level of your current life level. To do this, you must collect a certain number of decorations along the way, which are sold in special crates alongside a life-size cutout of Marina. These are the same decorations that are used in the hidden object style games. As you complete each level and complete all the challenges, you earn more money to be sent to buy more decorations for Fishdom H2O: Hidden Odyssey.