Hydrocity Zone

Hydrocity Zone is the second zone in Sonic the Hedgehog 3 (or Sonic 3 & Knuckles). This is the most water-filled level in the game, and several parts of the level takes place underwater. This is also the only level in the game to feature the air bubbles (except the bubbles inside the balloons in Carnival Night Zone), which prevents the character from drowning. However, if you find a water shield you don't need the air bubbles.

Sub-boss
The sub-boss this time around is Big Shaker, a spherical contraption with four rockets. This device spins back and forth through the U-shaped pit in which you are standing, before settling on a pole set in the middle of the arena. It's only safe to attack the device while it is in the middle, at which time it will have begun to turn the pole, which in turn stirs the water, and your character. However, you can Spin Dash up the side and attack while it is off-screen without getting hurt. Though the boss itself is relatively simple to beat, remember that Sonic & Co. can still drown while underwater.

Although the 30-second limit with surviving underwater is still true for this mini-boss, it is not possible to drown whilst the score is being tallied. This can be tested by, after defeating Big Shaker, keeping the goal sign from hitting the ground by jumping into it, whilst keeping the character below the water. Eventually the drowning music will start, but then if the goal sign is allowed to touch the ground, the music will fade away and the score-tally sequence will start. The warning sound is still heard every five seconds, but the player will not drown. The drowning timer is reset at the start of Act 2 as Sonic / Tails / Knuckles gets sucked under into the next part.

Boss
The Screw Mobile has a massive screw propeller attached to its underside, with which Dr. Robotnik can whip up the water into the arena into a tall vortex. He also drops mines from the back of the craft. Eight hits are required to defeat him.

Archie Comics
In the Archie Comics, it is known as Hydro City, where it is an ancient and abandoned underground city filled with water located underground on Angel Island. Constructed hundreds of years ago, it was supposedly constructed even before Echidnaopolis had been. In 3236, Knuckles the Echidna lead Monk there to evade being captured by Hunter, and eventually Knuckles managed to defeat the Overlander there, but not before Monk was killed. (KtE: #32)
 * Assuming Hydro City was built before Echidnaopolis, it would had to have been built under the ground and before the Floating Island was created.

Trivia

 * In the first act, statues resembling Sonic can be seen at the top of the background.
 * In the Wonderman music video by Right Said Fred a sign that says "Hydrocity Zone" is seen.
 * Some of the emblems seen on the walls of this zone closely resemble those seen in the Labyrinth Zone of Sonic 1, which is similarly water-filled.
 * In Sonic 3 & Knuckles, the rather unhelpful yellow spring that sends the player back in the section with the moving wall at the beginning of Act 2 has been replaced with an extra life.
 * This is the earliest zone by which all seven Chaos Emeralds can be obtained.
 * This is the very first level to have Sonic/Tails run over water.
 * Elements of this stage appear in Act 1 of Seaside Hill and Water Palace for Sonic Generations.
 * Hydrocity Zone's music is also collectable in Generations, under the name "Hydro City Zone".

Glitches

 * In Sonic the Hedgehog 3 (alone), during the mini boss, if Sonic (and/or Tails) stands underwater until the "Drowning" music kicks in, jumping out will play the Sonic & Knuckles miniboss music. This trick also works for the battle against Eggman. Sonic 3 & Knuckles has this glitch as well. Another thing worth noting about the mini boss is that in Sonic 3 (alone), the "Major Boss" music plays instead of the "Minor Boss" music. The Sound Test for Sonic 3 contains most of the music from Sonic & Knuckles, including its "Minor Boss" music; Sonic & Knuckles' Sound Test blocks out all Sonic 3 music.
 * In Sonic 3 (alone), during the fight with Eggman, if Sonic is Super Sonic and gets caught in the whirlpool that Eggman's machine creates, he will transform back into regular Sonic, but remains golden; his quills will drop down like normal. He also stops losing rings. This was fixed in Sonic & Knuckles.
 * In Sonic 3 (alone), when Knuckles destroys the bridge, hold down right on the D-pad. If you do correctly, Sonic will be able to bypass the battle with Eggman and head straight to the capsule (you have a higher chance of doing this if you're Super Sonic). Opening the capsule will clear the zone, but the game continues with Sonic doing his ending pose, and he won't be able to continue to Marble Garden unless you reset the game. Bypassing the capsule will let you, with the help of Tails, travel to the point where Hydrocity Act 2 "loops back" (repeats the level layout). It should be noted that unless you destroy the capsule, you can still go back and fight Eggman as normal, but if you open the capsule, and then defeat Eggman, the capsule won't be there! You can also perform this glitch by simply running to the capsule, and then running back to defeat Eggman. All of these glitches were also fixed in Sonic & Knuckles.