The water is an environment largely used in the levels. The water is always opaque.
The player can walk on the surface of the water with his body half-submerged.
While submerged, if the player gets out of air he will continuously lose health until he reach the surface. There exist the Scuba Gear item to prevent drowning.
Bullets (hitscan) cannot cross the water surface - actually realistic for real world physics - while large projectiles (non-hitscan) can. Strangely, bullets can cross underwater if they were already fired there.
Technically, the underwater part is an outside area of the level, which the player is teleported. This can easily be seem in the Auto Map function.
The last boss of the game, the Alien Queen, appears exclusively underwater and attacks the player electrocuting the water. Strangely, the attacks seems to reach any area out of water.
- If the player reaches an underwater sector from a surface sector and vice-versa through special methods (not using the submerging default engine), the video palette will not be assigned.
- The only stock level which this can be seen is The Queen, where the player can walk through water standing vertically.
- Loading a saved game will recover the palette of the current sector.
- Several machinery-based enemies were never supposed to appear underwater, they are the Recon Patrol Vehicle, Sentry Drone and Assault Commander; Sharks and the Alien Queen are supposed to be used only underwater. There is no stock level that will use them in any other manner, although user maps do sometimes contain them otherwise; while they work, they looks somewhere comical and odd. The demonstration level, Zoo, uses the Alien Queen outside water.
- Several enemies (Assault Enforcer, Battlelord and Cycloid Emperor) cannot enter submersive sectors. They can otherwise be spawned underwater.
- In Duke Nukem Total Meltdown exclusive level Nightmare Zone, one door sector is used underwater, which causes the water there not to work. The player will often "fall in air" in the out of water area and recover his breath preventing drowing or deactivate the Scuba Gear. The palette error can also be noted.