Underwater mines, or naval mines are self-contained explosive devices that are placed above water to blow up enemy vessels, or to be used as traps.
Several underwater mines were planted at the Zanzibar Fortress's waterways on its second basement floor.
Sons of Liberty
Underwater mines were planted in the B1 flooded area of the Shell 2 Core of the Big Shell by Vamp during the Big Shell Incident in 2009 as an way to deter the FOXHOUND agent Raiden from rescuing Emma Emmerich in the then-completely flooded passageways due to damage caused by one of Fatman's non-scented bombs earlier causing a leak. The mines were speculated by Solid Snake to contain built-in compound sensors that could track anything from something's acceleration speed to changes in the water pressure, and even body temperature, among other data.
Behind the scenes
The underwater mines, aside from Metal Gear Solid 2's main story mode, were also used in the Substance VR Missions as floating obstacles in various missions, including but not limited to variety missions that involve hanging.
In the TV spot for the French PMC Pieuvre Armement in Metal Gear Solid 4: Guns of the Patriots, seen when starting the game, underwater mines were seen surrounding a giant octopus, although it is unclear whether Pieuvre Armement itself actually used underwater mines.