Like other stages in Sonic Rush Adventure, the Hidden Islands must be located on the game's Sea Chart to unlock them. However, most of them cannot be seen on the Sea Chart (hence their name), meaning that the player has to locate them without guidance. Also, while some of the Hidden Islands are required to progress with the game's storyline, most are optional stages that do not have any impact on the storyline. It is only the obligatory Hidden Islands that are visible on the Sea Chart. Upon finishing a Hidden Island, the player may unlock missions in Marine's house on Southern Island (some of which are needed to collect the Sol Emeralds and unlock Deep Core).
Each Hidden Island, except for Hidden Island 16, is a fairly short and simple stage which can be completed in less than a minute. Their gameplay also tends to focus on a certain gimmick, level layout or gameplay style. Every Hidden Island also has a "theme", which includes the background music, scenery, Badniks, and gimmicks. Many Hidden Islands borrow their theme from one of the first five stages in the game (for example, Hidden Island 9 is similar to Machine Labyrinth). Others use the exclusive "Hidden Island" theme.