The Submerged World

Not to be confused with the Sunken Castle or Flooded Plains, similar levels found underwater.

The Submerged World is an anomalous level found in some personalized copies of Super Mario 64. The level usually replaces Wet-Dry World, though has been reported to replace Jolly Roger Bay and Dire, Dire Docks, though it can appear as it's own level instead. The level is described as an underwater city, similar to the town part of Wet-Dry World. The level reportedly shares it's theme with Jolly Roger Bay, though has also been reported to have the Hazy Maze Cave theme or a completely unique music track.

Geography
The Submerged World has been described as mainly being made up of several underwater buildings underwater, with several islands on the top of the ocean above them. There is also commonly tunnels connecting several buildings, as well as a temple or castle. Unlike Wet-Dry World, some reports say that the houses can actually be entered, though they are usually of minimal interest. Some common enemies are Bubs, Bloobers, Skeeters and a Unagi.

The castle is the main sub-area, reportedly being similar to the castle segments of Super Mario Bros. 3, with several more hazards and enemies such as Thwomps, Bullet Bills, Bob-ombs, Snufits, and Flame Spitters. It is usually accessible by draining the water in the level somewhere using the Crystal Taps from Wet-Dry World. The castle typically also has a boss of some kind, often being an Eyerok, though some people have reported a unique boss, a supposed "sea monster" that looks and acts like a Unagi except it actively chases after the player, and it has to be damaged by either running into a hazard or somehow draining the water.

A notable aspect of the Submerged World is that it seems to also add another area depending on what level it replaces if it replaces any at all, usually directly referencing the level it replaced, such as a sunken ship when replacing Jolly Roger Bay, or Bowser's submarine when replacing Dire, Dire Docks. This is odd, as they usually have minimal significance to the level, except for occasionally being tied to a mission.

Missions
The most common mission in the Submerged World is finding 5 treasure chests and opening them in the right order, similarly to the missions in Jolly Roger Bay and Dire, Dire Docks. The other common missions are reaching the end of the castle and beating the boss if it appears, and collecting 8 red coins. The other missions are a lot more varied, typically being tied to the islands or level-specific sub-area.

Theorizing
It has been theorized that the Submerged World was originally inhabited by people before being evacuated, either due to Bowser attacking with his submarine or a ship crashing into the city, depending on which level it replaces. This would explain the abandoned and run-down nature of the level. Alternatively, it just got flooded somehow and everybody left due to that.

This level has been speculated to be created through Dynamic Level Arrangement, due to it appearing to be a conglomerate of all 3 of the base game's water levels, particularly with the added areas based on level replacement. However, this doesn't explain the castle sub-area, which may indicate a yet to be properly documented castle level that went unused and gets utilized for the Submerged World.