A list of all Amphibious units in Supreme Commander is available here.
Amphibious describes vehicles which are capable of moving across both land and water. Some Amphibious units travel on the surface like a conventional sea vessel, some Hover just above the surface, and others cross the sea floor.
A Cybran ACU enters the water.
Amphibious units which travel on the sea bed become Submerged. This renders them invisible to surface Radar but detectable to Sonar and vulnerable to attack by Torpedoes. Amphibious units which travel on the surface share the properties of conventional surface vessels, being detectable by Radar as well as Sonar, and vulnerable to torpedoes.
Hovering amphibious units, such as the Riptide, move across water as they move across land, without actually touching the water, and as such are immune to attack by Torpedoes, but are still detectable by sonar.
In the case of structures, the Amphibious ability only enables them to be built on both land and water, rather than enabling them to move between the two. Also, probably to avoid problems, it is impossible to build structures on a water-land interface.
Amphibiousness is a highly useful attribute because it reduces the limiting effect of water on unit movement. For units that travel above the surface, it is almost completely eliminated.
Units that are Amphibious and travel on or above the water include the Salem Class, the Riptide, the Aurora, the Ascendant, the Asylum, the Blaze, the Zthuee, the Yenzyne, the Iashavoh, the Athanah and all Engineers. Units that are Amphibious and travel underwater include all ACUs and SCUs, the Wagner, The Brick, the Percival, the Othuum, the Galactic Colossus, the Fatboy, the Monkeylord, the Megalith and the Ythotha.
Salem Class units are amphibious, but are much less mobile on land.