Stages with an underwater theme have significant sections set underwater. Enemies tend to be modeled 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 levels 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. See: Underwater gimmicks.

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

• 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. This zone also incorporates elements of the ancient ruins theme.
• Scrap Brain Zone - Sonic the Hedgehog (1991) - Act 3 only; it also incorporates elements of the ancient ruins theme since the level is a different color-palette of Labyrinth Zone.
• Aqua Lake Zone, Sonic the Hedgehog 2 (8-bit) (1992)
• Chemical Plant Zone, Sonic the Hedgehog 2 (16-bit) (1992) - A primarily industrial level, Act 2 of Chemical Plant Zone is flooded with pink Mega Mack, which functions exactly like water.
• Aquatic Ruin Zone, Sonic the Hedgehog 2 (1992) - This stage also incorporates elements of the ancient ruins theme.
• Hidden Palace Zone, Sonic the Hedgehog 2 (16-bit) (Beta) (1992/2013) - This zone also incorporates elements of the ancient ruins and underground themes.
• Wild Water Way, SegaSonic the Hedgehog (1993) - This zone also incorporates industrial elements.
• Tidal Tempest, Sonic the Hedgehog CD (1993) - Past, present and bad future timelines incorporate an underground theme and an ancient ruins theme similar to Labyrinth Zone while either future timeline incorporates an industrial theme. The water is more noticeably lower in the Past, while water levels have drastically risen in either Futures.
• Aqua Planet Zone, Sonic Chaos (1993) - This stage also incorporates elements of the ancient ruins theme.
• Angel Island Zone, Sonic the Hedgehog 3 (1994) - This stage also incorporates elements of the forest and fire themes.
• Hydrocity Zone, Sonic the Hedgehog 3 (1994) - This zone also incorporates elements of the ancient ruins and underground themes.
• Carnival Night Zone, Sonic the Hedgehog 3 (1994) - This zone has an amusement theme, but also includes underwater areas in Act 2. This theme is removed when playing as Knuckles.
• IceCap Zone, Sonic the Hedgehog 3 (1994) - Mainly a winter themed stage, this zone contains minimal underwater areas in Act 2.
• Launch Base Zone, Sonic the Hedgehog 3 (1994) - Located in Act 2. This zone mainly incorporates elements of the industrial theme.
• Azure Lake, Sonic the Hedgehog 3 (1994) - This zone mainly contains elements of the ancient ruins theme.
• Tidal Plant Zone, Sonic the Hedgehog Triple Trouble (1994) - This zone also incorporates elements of the industrial theme.
• Lake Rocky, Tails Adventure (1995) - This stage also incorporates elements of the coastal theme.
• Cavern Island, Tails Adventure (1995) - This stage also incorporates elements of the underground theme.
• Labyrinth of the Sea, Sonic Labyrinth (1995)
• Blue Marine Zone, Sonic Blast (1996) - This stage also incorporates elements of the ancient ruins theme.
• Lost World, Sonic Adventure (1998) - This stage also incorporates elements of the ancient ruins theme.
• Aquatic Relix Zone, Sonic the Hedgehog Pocket Adventure (1999) - This stage also incorporates elements of the ancient ruins theme.
• Aquatic Mine, Sonic Adventure 2 (2001) - This stage also incorporates elements of the underground theme.
• Dry Lagoon, Sonic Adventure 2 (2001) - This stage also incorporates elements of the ancient ruins theme.
• Death Chamber, Sonic Adventure 2 (2001) - This stage also incorporates elements of the ancient ruins and haunted themes.
• Cannon's Core, Sonic Adventure 2 (2001) - Knuckles' section only. Also incorporates elements of the industrial and space themes.
• Ice Mountain Zone, Sonic Advance (2001) - This zone has underwater areas, but mainly incorporates the winter theme.
• Ocean Base, Sonic Advance 3 (2004)
• Twinkle Snow, Sonic Advance 3 (2004) - Similar to Ice Mountain Zone, this stage also mainly incorporates elements of the winter theme.
• Water Palace, Sonic Rush (2005)
• Aquatic Base, Sonic the Hedgehog (2006)
• Plant Kingdom, Sonic Rush Adventure (2007) - This stage also incorporates elements of the forest and coastal theme.
• Coral Cave, Sonic Rush Adventure (2007)
• Pirates' Island, Sonic Rush Adventure (2007) - This stage has underwater areas but mainly incorporates elements of the ancient ruins theme.
• Chun-Nan, Sonic Unleashed (mobile) (2009) - This Zone also incorporates elements of the East Asian theme.
• Apotos, Sonic Unleashed (mobile) (2009) - This Zone also incorporates elements of the urban and ancient ruins themes.
• Ocean Ruin, Sonic & Sega All-Stars Racing (2010) - This stage also incorporates elements of the ancient ruins and Green Hill themes.
• Lost Labyrinth Zone, Sonic the Hedgehog 4: Episode I (2010) - Act 3 only; mainly incorporates elements of the ancient ruins theme.
• Ocean Ruin, Sonic & SEGA All-Stars Racing (2010)
• Dolphin Resort, Sonic Free Riders (2010) - This course has an underwater segment, but mainly incorporates elements of the coastal theme.
• Tropical Resort, Sonic Colors DS (2010) - This stage also incorporates elements of the amusement theme.
• Aquarium Park, Sonic Colors (2010) - This stage also incorporates elements of the amusement and East Asian themes.
• Chemical Plant, Sonic Generations (2011) - This stage mainly incorporates elements of the industrial and urban themes.
• 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 Act 2.
• White Park Zone, Sonic the Hedgehog 4: Episode II (2012) - This zone is a hybrid of the amusement, underground, winter and underwater themes. The underwater theme dominates mainly Act 3.
• Burning Depths, Sonic & All-Stars Racing Transformed (2012)
• Tropical Coast, Sonic Lost World (2013) - This stage mainly incorporates elements of the coastal theme.
• Hidden Palace Zone, Sonic the Hedgehog 2 (2013) - This stage mainly incorporates elements of the ancient ruins and underground themes.
• Ocean Purification Plant, Sonic Boom: Rise of Lyric (2014) - This stage also incorporates elements of the industrial theme.
• Undersea Bolt, Sonic Boom: Rise of Lyric (2014) - This level also incorporates elements of the ancient ruins theme.
• Green Hill Zone, Sonic Mania (2017) - This zone mainly incorporates elements of the Green Hill and underground themes.
• Chemical Plant Zone, Sonic Mania (2017) - This zone mainly incorporates elements of the industrial theme.
• Hydrocity Zone, Sonic Mania (2017) - This zone also incorporates elements of the ancient ruins and underground themes.
• Angel Island Zone, Sonic Mania Plus (2018) - This level also incorporates elements of the forest theme.
• Green Reef, Sonic Speed Simulator (2022) - This stage also incorporates elements of the Green Hill and coastal themes.
• Lagoon City Zone, Sonic Superstars (2023) - This Zone also incorporates elements of the ancient ruins theme.