In the corner of the Worley Winery in the Farmer's Market, there is a round wedge of cheese with a piece missing next to six bullet holes. The arrangement bares a striking resemblance to Pacman and the pellets he eats.

A teleportation plasmid was planned for the first game but was cut, as it could be used to break the game's script during certain events. This plasmid was referenced as an Easter egg in Bioshock 2 in the Fontaine Futuristics level as an "Unstable Teleport Plasmid" that teleports around the level when the player interacts with it.

Before the Little Sisters became the "gatherers" in the game, early designs included a sea slug, a frog with a funnel in its anus, and a dog in a wheelchair.

During the game's opening, before the player obtains the wrench, Atlas will ask the player to find a weapon mentioning to "find a crowbar or something." This is a reference to the Half-Life series, in which the player uses a now iconic crowbar associated with the series.

The Little Sisters had a stage of development where they were mole-like creatures that scurried around Rapture collecting Adam.

There seems to be a blank sign and four little rectangular prongs floating right under the Bathysphere. It could be used for distance between the ground at the end, or a placeholder for when the Bathysphere was to be completed. It follows you from the start, all the way to the end of the little trip. It has no physics or textures.

One abandoned variant of the Big Daddy was the Slow Pro, also known as the SloProFum by the development team. It would maul players with an enormous hook and would fire iron bearings from a barrel. To fire its weapon, the Slow Pro would kneel on the ground and track the player. SloProFum stood for "slow projectile/fucked-up melee".

In the German version, a number of content in-game had been censored and altered:
• The less blood is seen. The pipe, for example, won't be stained with blood after hitting an enemy.
• Wounds on enemy corpses were removed.
• Telekenesis can't be used to pick up enemy corpses.
• Some hacksaws and blades were removed from corpses.
• The intro sequence was completely redone, just consisting of a series of in-game cutscenes.

The 2K Blog released a series called "Beyond the Sea", which in a 27th of July post explained that another Big Daddy was considered for the game. Dubbed the "Slug Bug", this Big Daddy had a amorphous slug-like parasite on its shoulders. Ultimately this design was scrapped and didn't go beyond the concept art stage.