Stages with an underwater theme have significant sections set underwater. Enemies tend to be modelled on fish or other aquatic creatures, but the main obstacle in underwater levels is the water itself. Since Sonic cannot swim or float, he runs along the bottom of the levels just like on land, except that he moves slower and must regularly replenish his air supply or else die by drowning. Air can be obtained by surfacing or by swallowing air bubbles. Partly for this reason, underwater levels are often the most difficult in a Sonic game.

Other common elements in underwater levels include water spouts that rocket Sonic to new locations, fast-moving flows of water that Sonic must either ride or resist, and rising water levels that Sonic must keep ahead of as a sort of time limit to certain sections.

The underwater theme is one of the most versatile in terms of setting, and can overlap with many other themes, including the ancient ruins theme, industrial theme, and winter theme.

Note that the fluid making up the level need not strictly be water. Chemical Plant Zone's pink Mega Mack has exactly the same properties.

Stages with an underwater themeEdit

• Labyrinth Zone, Sonic the Hedgehog (1991) - The first and arguably most famous example of the underwater theme, Labyrinth Zone (set in a submerged ruin) introduced most of the elements that came to define the theme. The third act of Scrap Brain Zone from the same game reused the Labyrinth tile set (though palette-swapped) and obstacles, and introduced pink Mega Mack.
• Chemical Plant Zone, Sonic the Hedgehog 2 (1992) - A primarily industrial level, Chemical Plant Zone is flooded with pink Mega Mack, which functions exactly like water.
• Aquatic Ruin Zone, Sonic the Hedgehog 2 (1992) - Aquatic Ruin Zone, again combining underwater elements with an ancient ruin setting, is a rare example of an underwater level immediately following a previous underwater level, coming as it does immediately after Chemical Plant.
• Hydrocity Zone, Sonic the Hedgehog 3 (1994)
• Carnival Night Zone, Sonic the Hedgehog 3 (1994) - This zone has an amusement park theme, but also includes underwater areas.
• Tidal Plant Zone, Sonic Triple Trouble (1994) - This zone also incorporates elements of the industrial theme
• Lake Rocky, Tails Adventure (1995)
• Cavern Island, Tails Adventure (1995)
• Ice Mountain Zone, Sonic Advance (2001) - This zone has underwater areas, but mainly incorporates the winter theme.
• Water Palace, Sonic Rush (2005)
• Aquatic Base, Sonic the Hedgehog (2006)
• Dolphin Resort, Sonic Free Riders (2010) - This zone has underwater areas, but mainly incorporates the coastal theme.
• Aquarium Park, Sonic Colors (2010)
• Lost Labyrinth Zone, Sonic the Hedgehog 4: Episode I (2010)
• Chemical Plant, Sonic Generations (2011)
• Seaside Hill, Sonic Generations (2011) - The underwater theme is featured in Act 1, but the coastal theme is also used in Act 2.
• Sylvania Castle Zone, Sonic the Hedgehog 4: Episode II (2012) - This zone is a hybrid of ancient ruins theme and the underwater theme. The underwater theme predominates mainly in the second act.
• White Park Zone, Sonic the Hedgehog 4: Episode II (2012) - This zone is a hybrid of the amusement park theme, the winter theme, and the underwater theme. The underwater theme predominates mainly in the third Act.