Underwater Boss Battle

Water based levels in games have an odd reputation. They can be seen as the greatest thing ever, if handled well enough, or the worst possible section(s) of a game. But in these levels, assuming the game itself generally has boss fights at all, the inclusion of water in the arena can radically change a boss battle and how it plays out. If handled well, it can easily be a clear example of the best boss in the game. It can also be seen as That One Boss in the opposite scenario. Nevertheless, underwater boss battles (or generally water based battles in general) have a LOT of different possible designs, and as can be seen via the examples below, have been a standard change to the traditional Boss Battle formula since the beginning of gaming in general.

Underwater Boss Battle
The entire arena is underwater, and the boss (as you can probably figure out) is an aquatic creature that cannot survive on land. Usually not one of the more favoured battles by players, as the changed controls underwater may make the battle quite a bit tougher than it needs to be. Common types of enemies for this are usually sharks, eels, various forms of octopus, etc.

Action Adventure

 * Morpheel from The Legend of Zelda Twilight Princess.
 * It's also possible to fight Gyorg of Majora's Mask in this fashion, though the platform boss (see below) is also an option. The safest method is to stun Gyorg from the platform, then dive in to damage it as a Zora.
 * Angler Fish, the boss of the fourth dungeon in Link's Awakening, is an underwater sidescrolling boss.
 * Plasmarine, the boss of the seventh dungeon in Oracle of Ages, is also fought underwater.
 * The aforementioned Angler Fish also returns to serve as the mid-boss of this level, though for some weird reason even though the background suggests that you're underwater you control Link as if you were on land.
 * Every boss in the Ecco the Dolphin series, but seeing as pretty much the entire game takes place underwater, this is hardly surprising.
 * Castlevania: Portrait of Ruin has Dagon, some kind of weird reptillian... thing. You fight him underwater, and one of his attacks even involves taking away all the water temporarily in order to use it like a weapon.
 * Jaws Unleashed for Xbox, surprisingly, the game only had a few bosses that actually were completely underwater. The most notable was the giant squid. The NES game has you fighting the shark underwater, like everything else.
 * An Untitled Story features DeepDragon, a static, ice-breathing sea serpent.
 * Shark from Clash at Demonhead. His base is underneath the sea on Route 22, which you'll need an Aqua Lung to reach (and survive).

Action Game

 * Bomberman Hero featured some levels with Bomberman turning into a vehicle. One of these was the Bomber Submarine. Essentially crappy shoot-em ups, they featured simple bosses at the end. The bad part: well, the boss rush at the end features an underwater re-encounter with a stone lion for no real reason. The weird controls added to a grand total of 5 health units made this battle a living hell.
 * Monster Hunter Tri adds underwater fighting, and thus underwater bossfights. Normal monsters will go back on land once tired from raging too much, but the final boss

Beat'Em Up

 * Mech Taco from Captain America and The Avengers. (No, it's not a taco. Think Gratuitous Japanese.)

First-Person Shooter

 * The Alien Queen in Episode 4 of Duke Nukem 3D. Not only is she 2000 hit points tougher than the other bosses, you have to fight her underwater, she can give you a nasty zap, and she keeps laying more enemies!
 * The penultimate boss in Duke Nukem Forever, the Energy Leech. Easily falls under That One Boss thanks to Duke's slow swimming speed.

MMORPGs

 * Maws, from World of Warcraft, is summoned out in the sea. The raid composition determines whether he's fought at the water's surface or underneath
 * Also from World of Warcraft is The Lurker Below, the second boss of Serpentshrine Cavern. While he's mostly fought on platforms (due to the fact that the water is hot and deals damage over time while you're in it), you're forced to go underwater every so often in order to avoid his Spout attack, which will knock you 100+ yards away into the boiling water, probably causing your death as you try and swim back to the platform.
 * In Adventure Quest Worlds, you get to battle a Nessie as an underwater boss battle for the third boss fight in Arcangrove.
 * Similarly, the Deep Dweller is another underwater boss battle that also serves as a third boss fight in a different area, this one in Etherstorm Wastes.

Platform Game

 * Kingfin from Super Mario Galaxy.
 * Also the Octopus boss from Super Mario Land 2.
 * And a giant Blooper Mini Boss in Super Paper Mario.
 * The second battle against Wendy O. Koopa in New Super Mario Bros Wii. The basic gist is that Kamek has submerged the arena; considering that you can't stomp on enemies underwater, you have to hold out until the water level becomes low enough for you to jump on Wendy.
 * Don't forget the ubiquity of this trope in romhacks. Take a wild guess which hack started this trend.
 * Eely-Mouth from Super Mario Sunshine, interestingly enough the only underwater boss in a water-based game.
 * Barbos from Donkey Kong Country 3.
 * And Davy Bones from Donkey Kong King of Swing.
 * The defence wall type minibosses from Wario Land Shake Dimension.
 * The Hulking Lungfish in Psychonauts is an underwater enemy whom you fight from within an air bubble. Since Raz can't swim, you have to figure out how to damage her without leaving the bubble. Eventually, though, she leaves the bubble and starts attacking you as normal.
 * Banjo-Kazooie-Tooie has an anglerfish of the type 1 variety named Lord Woo Fak Fak. You can actually fight him as the submarine transformation in this level or as bear and bird.
 * Many Robot Masters from the Mega Man games, including the first-ever Robot Mistress, Splash Woman from Mega Man 9. Also Bubble Man from Mega Man 2 and Dive Man from Mega Man 4. Since the main effect of water is super-high jumping, they usually put insta-kill spikes on the ceiling.
 * In Mega Man X, Launch Octopus among others.
 * Similarly, Doujin game Rosenkreuzstilette has you fight Trauare Wrede underwater or above water depending on which path you take in her stage.
 * In Rayman 3: Hoodlum Havoc, the boss of The Land of the Livid Dead is a Hoodlum piloting a giant underwater mecha.
 * A few examples from the Sonic the Hedgehog series include:
 * Sonic CD's Tidal Tempest fight against Eggman's Eggmobile. Eggman is kind of gentle to be surrounded by bubbles Sonic can breathe through...
 * Sonic the Hedgehog Triple Trouble's Tidal Plant Zone against Knuckles (!).
 * Sonic Colors's fight with Admiral Jelly in Aquarium Park.
 * Sonic Rush Series's Water Palace with Eggman's Egg Turtle is another example where you actually can't drown, though occasionally the water level will drop.
 * Draygon/Botwoon in Super Metroid and Alpha Blogg in Metroid Prime 2: Echoes.
 * Ty the Tasmanian Tiger 3 has you battle a giant green mutated crab while underwater. Notably, your air meter is also your Life Meter, and both are replenished by surfacing or swimming into jets of bubbles. Since there are five such jets in the arena, it is literally impossible to lose.
 * The hammerhead shark in Ristar. Hitting it would knock it into a cork which would lower the water level. After knocking out all the corks, all the water is drained and you win, but until that point it just gives you less room to swim around and dodge his attacks.
 * Drawn to Life has an anglerfish boss that is fought entirely underwater.
 * In Kirby's Dream Land 3, Acro the orca starts off as a land-based boss until he destroys the floor and begins the second phase in an underwater arena. He also appears in Kirby 64, but this time the whole fight takes place underwater.
 * Before him, there was the angler fish Sweet Stuff, from Kirby's Dream Land 2.

Role Playing Game

 * King Kuraselache (boss of the First Epoch) and King Rogon (one of the bosses of the Fifth Epoch) in EVO Search for Eden, a great white shark and a Gillman respectively.
 * Kingdom Hearts had Ursula, an underwater battle.
 * In Romancing SaGa, one of the Evil Minions of the Big Bad ambushes you after getting the Cosmic Keystone from the Underwater Temple
 * In Romancing SaGa 2, you actually fight Subier either underwater or on a boat depending on your actions.
 * Final Fantasy VII has Emerald WEAPON, an optional boss who hangs out at the bottom of the sea. And you don't even fight him in your submarine. There's also a couple of underwater (though air-containing) areas.
 * All of the boss fights in the Atlantis mission in the first Marvel Ultimate Alliance game, including Tiger Shark, Attuma, and the Kraken.
 * The Giant Slaughterfish in The Elder Scrolls IV: Oblivion, which you encounter during the Thieves' Guild questline.

Shoot'Em Up

 * Star Fox 64 featured the giant clam boss in Aquas, the underwater level, while piloting the submarine vehicle exclusive to the level
 * The boss of Zoness is a submarine, though battled at the water's surface while in the Arwing
 * Ultimate Crab Battle. The entire games takes place in a boss battle against a Giant Enemy Crab, who has a ridiculously high variety of special attacks mostly based on gadgets he pulls out of himself, hammerspace style.
 * In the Hunt has five of its six boss battles like this. Then again, your character is a submarine, so it's not surprising.

Above Water Boss Battle
The player is on a platform or more above the water. Usually, the boss is either in the water and attacks from there, jumps out of the water at the player from under the floor, or (in the case of Morpha in The Legend of Zelda Ocarina of Time) pretty much IS the water.

Action Adventure

 * Morpha from The Legend of Zelda Ocarina of Time.
 * Gyorg from The Legend of Zelda Majoras Mask.
 * The final bug boss in Lanayru in The Legend of Zelda Twilight Princess
 * Phytops from Spirit Tracks.
 * Overlord has a large sea serpent that sticks its head out of the water and attacks you while you're on land. Although since you see more than one throughout the game, I'm not sure if it qualifies as a boss. Still, the first time you face it feels very much like a boss battle (no way out until it's dead, have to use new things gained during the level to defeat etc).
 * Shadow of the Colossus has 2 water-based colossi battles. One is the terrifying electric eel, and the other is a later fight with a colossus who walks around a lake. The first one is unique in that the boss itself is the only platform in the arena, and it tends to drag you underwater, too.
 * Castlevania: Chronicles of Sorrow has an unusual case in the form of Rahab, a large fish of some type. The area where you fight him is a pool, and there are no platforms for your hero to stand upon(he instead floats on the surface of the water), but the boss will frequently leap out of the water to attack in one of three ways. Defeating it nets you the ability to move around underwater.
 * Rahab from Legacy of Kain: Soul Reaver is a straight example. He swims around, Raziel jumps between 8 pillars while Rahab shoots water at him or tries to bite him.

MMORPGs

 * Maws, from World of Warcraft, is summoned out in the sea. The raid composition determines whether he's fought at the water's surface or underneath
 * The Lurker Below in Serpentshrine Cavern, must be fished out of a pool of water (it's a gigantic sea monster sort of thing) to initiate the battle. The raid's preparation determines whether the water around it is filled with flesheating bastardly fish (bad) or boiling (not as bad), so it's generally advised to stay on the solid ring around the boss' pool.

Platform Game

 * Cheepskipper from New Super Mario Bros
 * Kroctopus from Donkey Kong Country 3.
 * Possibly Catbat from Wario Land 4.
 * Metroid Fusion has Serris. It jumps out of the water frequently, its entire attack pattern revolves around snaking in and out of the water while you either try and dodge from one of several platforms or hang on an overhead ladder on the ceiling and try and avoid from there.
 * The second B.O.X fight - This time you're on a overhead ladder across the ceiling while it stays in the water, electrifying it, while occasionally jumping at you and shooting missiles.
 * And Nettori just kind of stands there above the water, but the water has deadly plants growing in there which eat you alive and make it difficult to get out of the water if you fall into it.
 * The Chykka larva from Metroid Prime 2 swims around in toxic water while you stand on a platform. You can attack it while it's swimming, though it's very hard to hit. He does occasionally jump out of the water and also occasionally jump onto onto the platform partially to try to eat you.
 * Fatty Whale from Kirby Super Star and its remake (Super Star Ultra) attacks either by bouncing atop the floating platform Kirby's standing on or by swimming around said platform while attack.
 * The grotesquely hideous Jinmen-Gyo (Man-Faced Fish) from the 4th stage of Contra: Shattered Soldier. It attacks by jumping out of the water, trying to eat the player from one of three floating platforms, as well as sucking the platforms into his mouth in a bid to swallow the player alive.
 * Planet Wisp's Rotatotron in the DS version of Sonic Colors is above water while you are too, but its major weak spots are underwater, only reachable by use of the drill wisp.
 * Sonic the Hedgehog 2 has two bosses like this, neither of which actually involve water:
 * Hill Top Zone's Flying Eggman Mech jumps up from a lake of lava, spits a fireball, then dives back in post attack. Hitting it doesn't hurt you, but hitting the lava does
 * Oil Ocean's Flying Eggman Mech 2.0 also comes up from below periodically, after spending a while attacking with a spiked claw and a laser gun from under the oil. You can actually jump into the oil and as long as you keep jumping, you won't sink to your death
 * The Stage 2 boss of Alisia Dragoon.

Shoot'Em Up

 * Einhander has Salamander, the amphibious stingray submarine with a pair of arms. It attacks you from the water during the first half of the fight... after which it gets out of the water to attack you while hanging from two bars above..

Stealth Based Game

 * Vamp in Metal Gear Solid 2: Sons of Liberty, kind of. He'll swim through the water in the room, but only attack you when above it.

Boat Based Water Boss Battle
Your character is riding in a boat or similar vehicle on the surface of the water while the boss attacks from the actual lake/river/whatever type. Also counts any races or events against water based boss characters that involve said boat or vehicle usage on the surface.

Action Adventure

 * Bahamut from La-Mulana is of the boat-based variety, with the annoying caveat that you can fall out of the boat.
 * The boss battle against "Sapientia" has Bayonetta surfing on a piece of scrap metal in the middle of the ocean while Sapientia tries to attack from underneath her. During the last section of the fight, the battle is fought in a giant whirlpool.
 * Castle Crashers has the river rapids level where you surf on top of logs, rafts or even corpses against a giant Catfish.

Action Game

 * In Jaws for NES, the very definitive final battle against the giant shark requires you to

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 * De Rol Le in Phantasy Star Online.
 * Though, for all intents and purposes, it's basically just a large platform surrounded by water, since the raft is so big that it takes several seconds just to run across it. You may be moving, but the only way this affects the battle is that De Rol Le often swims alongside (or in front of or behind) the raft. Regardless, the arena doesn't affect the gameplay much, except that the boss' submerged parts are invulnerable.
 * Very much trivialized if you brought a gun. Seriously, when it hovers it one place, it just screams "FIRST PERSON-SNIPE ITS ASS!!!"

Platform Game

 * Donkey Kong 64 has the player, as Lanky Kong, motor around in a boat while navigating a maze of electrified bouys during the battle with a giant pufferfish.
 * Diddy Kong Racing features a boss race against an octopus.
 * The second boss of Super Ghouls 'n Ghosts, the Kraken, is fought from a tiny raft.
 * Bug!! has the third boss, a swamp worm. You ride a platform floating on the water, once the boss takes enough damage, the platform sinks, and then you have to Goomba Springboard on the boss' body onto an even smaller platform. Getting hit once will probably result in Bug falling off and drowning instantly.

Role Playing Game

 * Mega Man Legends has MegaMan fighting against Tron's Frog Bot at Lake Jynn while he's riding in a boat he got from Wily's (no relation to the Mad Scientist of the original series).

Survival Horror

 * Del Lagos of Resident Evil 4 is fought while on a boat, using harpoons if I'm not mistaken.

Third-Person Shooter

 * Gears of War 2 features the Leviathan, a Kraken/piranha mix that tried to drag your boat down, then eat it whole.

Character in Water, Boss Above Water
Your character is in the water, the boss is above the water.

Action Adventure

 * Castlevania: Order of Ecclesia has a boss with waist/ankle deep water. The boss floats on top of the water, and attacks you, sometimes summoning giant tidal waves.

Platform Game

 * Sonic the Hedgehogs Labyrinth Zone boss qualifies, though it is more of a race against rising water, so if you go fast enough, none of the battle will be spent underwater. Which is hard to do. Sonic the Hedgehog 4s Lost Labyrinth level, being based on the original Labyrinth Zone, also does this.
 * Both Hydrocity Zone bosses in Sonic 3 and Knuckles. For Act 1, the water is deep enough to drown in, and the boss stirs up the water to knock you off your feet. For Act 2, the water is waist-deep, and Robotnik uses it to try and pull you into a whirling propeller.
 * Sonic Advance Trilogy later featured a fight where most of the arena is filled with water and Robotnik hovers around the top of the screen, necessitating a stepping-stone strategy to reach him or simply catch a breath.
 * Jet Stingray in Mega Man X 4.
 * Mega Man 3 has a Mook Maker that drops turtles into the pool Mega Man is in. Destroying the turtles destroys the boss.
 * The battle with Mega Water.S in Mega Man: The Wily Wars, though the opening of the battle gives you the impression that it would be a straightforward underwater fight.

Shoot'Em Up

 * The Shoot'Em Up In the Hunt has a Stationary Boss robot boss that hung from the ceiling above the water in its first phase. Thing is, your character is a submarine that can only travel about the water, so you had to surface and use your anti-air weapon to damage the boss.

Stealth Based Game

 * In Metal Gear Solid 3, it's possible (and easy) to fight The Pain this way.

Action Adventure

 * In the battle against the Living Core in Cave Story, the water goes up and down.
 * Octogon, the boss of the sixth dungeon in The Legend of Zelda: Oracle of Ages, moves its weak spot below the surface when hit from the platform and back above the surface when hit underwater.

Platform Game

 * Demonic from Purple is normally a waterless battle, but he can raise water into the room in an attempt to electrify you.
 * Sonic Rush Adventure's Coral Cave boss, the Ghost Kraken, is mostly above water, but sometimes it drags you and the platform down to fight you underwater for a bit. Like the Rush example above, you can't drown. Bizarrely, the first part of Sonic the Hedgehog Triple Trouble's first boss, the Grand Motobug, has you underwater and the turtle boss above water, but you can jump out to hit him.
 * In Mega Man X7, both the player and Splash Warfly start off above water, but Splash Warfly's modus operandi is diving into the sea and reappearing from random locations to attempt a sneak attack. Trying to follow his example will get you killed.
 * In Rock Man 4 Minus Infinity, the battle against Dive Man starts off this way, but he and Mega Man can jump up to the platform above the aquatic arena.

Role Playing Game

 * One of the early boss battles of Final Fantasy VI is against Ultros while riding a raft. The GBA remake also adds Leviathan as a Bonus Boss, who is fought underwater.
 * Monster Hunter Tri features underwater locations for the first time and, as you would expect in a series dedicated to the slaying of giant monsters, a number of underwater creatures have been created, the majority of them can come onto the land for periods of time too but the final offline monster is completely waterbound.
 * Ceadus. As soon as you jump into the water, you're there unless you use a Farcaster or faint. Protip: Mega Air Philters work wonders.
 * Plesioth, for example, from 2nd gen games in addition to Royal Ludroth, Gobul, and Lagiacrus from Tri.
 * Jhen Mhoran. However, Jhen plays this a bit weirdly, as he swims through the sand in a desert. Does this stop your courageous hunter? Not in the slightest! Just hop aboard the Dragonship and sail along side him! Specialized weapons are provided as well, such as ballistas, cannons, and the Dragonator.

Wide Open Sandbox

 * The boss battles with the orca and Giant Squid in Jaws Unleashed.