Mystery of Shark Island is a hidden object game where the player must find shells and pieces of artifacts, half-buried in the beach sands of an archipelago. The plot is told through a series of sketch drawings with text that pop up on certain points in the game. The main character wakes up on a island, washed ashore with a broken arm besides a magic box that exchanges shells for keys.
The main game screen is divided in two, the top portion showing the island shore covered with beach sand, shells and assorted flotsam and jetsam. The bottom portion is dedicated to the interface, showing the box and its strange cravings. At the start of each stage, a wave washes the beach and two sliding doors open up revealing the required items to complete the level. Most objects are shells and the occasional piece of bass relief, that must be found and clicked on the beach before the next wave comes.
The objective of each level is to reach a set amount of points, shown at the left side of the box. Several correct clicks fill a conch-shaped streak meter that multiplies the points, while wrong clicks reset it. A blue meter shows the time remaining before the next wave. Picking objects of the same type in a row gives extra points. Some objects are covered with a layer of sand that must be brushed aside before they can be collected.
Some power-ups coins appear randomly on the beach. The wind coin blows all useless objects from the screen. The super brush coin cleans all the sand covered objects of the beach. The strength coin makes lifting heavy rocks easier. The power lift coin takes away all heavy rocks from the beach. The hourglass coin increases the time before the next wave.
At the end of each stage, the box reveals and stores a key on slots at the top. These keys are used after the final level, to rotate the segments of a circular jigsaw puzzle.