Like the scraplets, a kind of mechanical pests/parasites who attacked The Transformers, in the Marvel comic books. Discovered accidentally when a human dropped a glass of water on an infected autobot.
Sometimes the audience will complain that anything so severely vulnerable to water shouldn't be able to survive in our atmosphere what with all the water vapor. Whether or not they're correct is debatable and as-of-yet impossible to prove.
In any setting containing monsters that are vulnerable to holy water — vampires, demons, etc. — a blessing and a Supersoaker are your best friends. True professionals bless rainclouds.
The Lost Boys used supersoakers filled with holy water to deadly effect upon the vampires of the movie.
In Constantine they did exactly something like this: They blessed the water tank of a Sprinkler System. Cue hurt demons...
Also happened in the Viva Las Buffy comic book, performed by a drive-in wedding priest no less.
Dungeons & Dragons has a high level spell to bless rainclouds, which combines very nicely with Control Weather.
Many accounts of mermaids have them doing this, particularly if they are harmed, harassed, or rejected by humans. On the other hand, if humans are nice to them, they will usually be quite nice back.
Anime and Manga
In One Piece, Sir Crocodile is made of sand that can freely disperse and reform when struck. When wet however, the sand clumps together so his face can be punched in. Furthermore, any devil fruit user can be defeated if they can be submerged in sea water (a problem for a pirate-themed adventure on a planet with even more water than the Earth), especially if they are so nasty they don't have friends inclined to help them.
In Bleach, Lunuganga, the Hollow made of sand, suffers of this weakness.
In the manga adaptation of Kingdom Hearts: Chain of Memories, this is how Sora, Donald, and Goofy defeat Larxene: Donald casts a Blizzard spell that Sora melts with a Fire spell while Goofy spins them around, creating a sprinkler effect that drenches Larxene and, due to her electric nature, causes her to explode.
In one episode of Sailor Moon, the Monster Of The Day is a confectionery-based drone called Marzipan. She easily manages to get the best of the Senshi by incasing them in sweets, until Sailor Mercury manages to attack her with Shine Aqua Illusion. It causes Marzipan to become soggy and heavily weakened enough for her attacks to wear off.
Very nearly happens to several characters in Cardcaptor Sakura in the episode dealing with the Watery Card. The card spirit itself is also shown to be very tempermental. Additionally, since it is of The Four Elements, it's more powerful than most of the other Card Spirits.
In Amakusa 1637, a group of captured Japanese Christians is taken to the Unzen Valley. The catch is that there are pools of very hot sulphuric water in Unzen, so they'll be tortured to death there. In fact, Natsuki and Eri walk into some jailers already torturing a man like this and attempt to confront them, but the one who saves the day is Eiji Horie since he uses a trick to create the illusion of a rising dragon., which terrifies the superstitious torturers as they believe they've angered the local gods. It's actually inspired in a Real Life case; see below.
Later, this is used in the form of a Drowning Pit where a pregnant woman and Eiji's love interest, the local Hooker with a Heart of Gold, are locked in. Which is actually the rendition of the incident that sparked the Shimabara Rebellion as a whole.
Used in Detective Conan, specifically in the case known as Billionaire Birthday Blues. Years ago, the Rich Bitch Reika and her Upper-Class Twit boyfriend Nikaidou saved themselves from a storm that crashed their boat via basically leaving the Rich Bitch's childhood friend Yaeko, who had come to help them, to drown in the sea. The guy who was in love with poor Yaeko, Ichieda, decided to take revenge... via murdering the two and using water as his "Weapon of Choice". In the present he strangles and drowns Nikaido, then he kidnaps Reika and puts her inside a makeshift Drowning Pit that he built in a deep Japanese bath tub, Bound and Gagged so she cannot escape. (As a bonus he drugs Ran and forcibly puts her head inside a water full sink so he can give himself an alibi... which only manages to ROYALLY PISS CONAN OFF and give him the first clues needed to take Ichieda down.
Also used in another case, where another Upper-Class Twit, Teruhiko, tried to get away from his soon-to-be Unwanted Spouse Shinobu via drugging the girl and leaving her to die by drowning inside a water park's closed section. The Detective Boys and Conan, however, found the unconscious Shinobu when they snuck into the spot, and from then on they worked in tandem to both save themselves and Shinobu and reveal Teruhiko's intentions.
In The Wizard of Oz, (in the film version, anyway) The Wicked Witch of the West is really susceptible to death by being splashed with water.
Parodied in a Futurama episode: "Who would have thought a small amount of liquid could ever fall on meeeeee...!" Leela turns herself into a witch a bit later, and meets the same fate almost immediately...due to a backed-up toilet.
In Dark City John Murdoch kills Mister Book by telekinetically smashing his human host body into and through a water tower, killing the hydrophobic alien within. How a hydrophobic parasite could possibly live inside a being made up of roughly 70% water is a different matter entirely; since they inhabited dead bodies, salt and preservatives may have been involved. Squick.
In the movie adaptation of The Day of the Triffids, the titular plants dissolve when blasted with salt water. It probably wasn't on the producers' minds, but this is a direct reversal of the original book, in which flame-throwers are among the most effective anti-Triffid weapons.
In Freddy vs. Jason, Freddy is able to finally break through the unstoppable resolve of Jason Voorhees by tapping into his innate fear of water (brought on by being a drowning victim in life).
Water turns out to be deadly to the aliens from Signs. Many consider this plot point to be idiotic: Why the heck were the aliens invading a planet 70% covered in poison, while naked no less? (We have a few theories.)
Another example of water proving fatal to aliens: the blob-like energy aliens in Night of the Big Heat can't be harmed with bullets or dynamite, but die at the end because their constantly heating the island up to suit their preferred climate causes a torrential downpour which melts them.
The villainous monster Barugon (Not to be confused with Baragon) is killed when Gamera throws him into a lake causing him to drown since water hurts Barugon and he cannot swim.
The Kid kills Death in Six String Samurai with water, realizing his weakness after spitting in his face causes him to scream in pain, as the saliva burns him like acid.
Lilo & Stitch: While water itself isn't deadly to Stitch, he can't swim and is too heavy to remain buoyant even in salt water. Naturally, he winds up on the most isolated chain of islands in the world. The series shows that Stitch's greatest fear is, in fact, deep water.
That's not all. Several of his "cousin" experiments could also be nullified through water, although they also needed water to be released from their capsule.
In The Movie, from a distance it looks like Stitch's ship is going to crash into the middle of the Pacific, and all the alien races there cheer as they assume he will fall into the ocean and drown. Then they zoom in and see that he manages to make landfall on a little tiny island chain. Much frustration ensues.
In Alienł, the creature is doused with molten lead, but manages to get out of the foundry; immediately thereafter, he is sprayed with water from a sprinkler system. The resulting thermal shock causes it to explode.
In Tank Girl, the Big Bad CEO of Water & Power has himself turned into a cyborg with a saw-bladed arm and a holographically-projected face. This makes him nearly indestructible ... until Rebecca dumps water on him and shorts out his circuits.
That technically didn't kill him, just temporarily incapacitate him. It was her stabbing him with the same dehydration tool he'd use to kill two or three others (on-screen at least) in the movie that did him in. So... Kill him without water?
Both monsters in Frankenstein Meets the Wolf Man meet their apparent demise when one of the local townsfolk blows up a dam near the ruins where the two are fighting.
The T-Rex breed of Sharptooth from Land Before Time are unable to swim due to their tiny arms. This allowed the heroes to kill the original Sharptooth, drowning him in a lake.
In Dune, Shai-Hulud is poisoned by water in large amounts.
In The Wonderful Wizard of Oz, a point is made about water being the only thing the Wicked Witch fears more than the dark... and yet she specifically has Dorothy (at this point her slave) cleaning her castle with water... This manages to be even dumber than the movie, where a bucket just happens to be lying around.
One of the Mooks in Skulduggery Pleasant uses magic to make himself invulnerable to fire. Unfortunately, it balances out with an extreme vulnerability to the opposing element...
Vampires are also somewhat vulnerable to water; ingesting salt water causes their throats to close up, which will probably suffocate them. It is lampshaded that this weakness isn't particularly useful for fighting them. One character is seen to have carried around a vial of saltwater for decades after surviving an encounter in his youth, only for someone to point out that he probably wouldn't be able to get the vampire to swallow the stuff before it finished him off.
The various species of terrestrial mantis shrimp found on Henders Island in Fragment are vulnerable to salt-water. Not just vulnerable to it, terrified of it. However, this could be considered a subversion, as it is not the water itself that kills the creatures, but rather their inability to regulate salt when it is introduced to their bodies. This fact is used heavily in the plot of the story from explaining why none of these Death World natives haven't gotten off the island and killed us all yet, as well as who sent the emergency signal that brought the boat to the island in the first place and started the whole story. One of the character's actually lampshaded this similarity to the Triffids, another group of creatures suceptible to the kill it with salt water tactic.
In fact, this is only the second permanent Golem death encountered in the series thus far.
In the Enchanted Forest Chronicles, wizards can be (temporarily) melted by splashing them with water, mixed with soap and lemon juice. The discovery was completely by accident, and nobody's completely sure why it works, but it takes all three elements to do the job; in a later story, Prince Mendanbar forgets the lemon, which just results in wet, soapy wizards, until Cimorene reminds him.
This was discovered by Alianora, Cimorene's fellow (and actually captive) Princess while the two were cleaning. This trope is also reversed when the Stone Prince throws water on the wizard who is holding the witch Morwen hostage. The wizard melts; Morwen, who practices clean living, does not.
In the Known Space series by Larry Niven, Martians were spectacularly vulnerable to water. There was a short in which explorers sent to Mars discovered an ornately constructed water well... and realized that it was used as a crematorium. That vulnerable.
The Veleek, a nearly unstoppable cloud of dust from Animorphs that can shred any solid matter by touch, is defeated when the kids trick it into falling into the sea.
In the vampire novel They Thirst, it is eventually discovered that seawater has a deadly effect on vampires.
Warden Carlos Ramirez from The Dresden Files is a water mage and combat magic specialist. In the Dresdenverse, water is associated with entropy and cleansing, and pretty much all of Ramirez's combat spells involve disintegration to some extent.
It is strongly implied that in Something Wicked This Way Comes, the Dust People might have this weakness. They must leave before the autumn storms because "the rain washes away their dust."
Live Action TV
The fiery Pyroviles from the Doctor Who episode "The Fires of Pompeii" (or the lesser foot soldiers, at the very least) are able to be killed by having water thrown at them.
In the short-lived UPN series Deadly Games (which involved a video game being brought to life, and Christopher Lloyd being evil), one of the villains was burned by water.
Power Rangers Mystic Force had the utterly invincible lava-based villain Magma. He spent the whole episode effortlessly handing the Rangers' butts to them, and then Madison gets pissed at her lack of screentime (no, seriously) and blasts him with a water attack... which burns him. (However, that's not what kills him - he then goes giant and resumes the buttkicking against the Rangers' Humongous Mecha, but is defeated by the rules of his own game with the Rangers, which must be obeyed even to the death.)
The 'Frogs' in Raumpatrouille can live in vacuum just fine and aren't bothered by energy weapons (at least not the small portable models used by humans in the setting), but oxygen is lethal to them. This is why they bothered to depressurize the human outpost where they are first encountered instead of simply leaving it as-is, which in turn is what eventually clues the protagonists in to their Achilles' heel.
In the Buffy the Vampire Slayer episode "Something Blue," Xander and Anya are attacked by a demon that can only be killed by drowning. They force his head into an inexplicably filled sink, creating smoke and killing it.
Another episode had Buffy kill a vampire by switching his glass of water with holy water.
Deadliest Catch, natch. Since the water they are in is near freezing, falling in could cause death within minutes with complete and utter disregard to your ability to swim. A rescue has to happen pretty much immediately, and that is made extremely difficult by the rough conditions of the Bering Sea.
''Supernatural: demons are highly susceptible to holy water, as you'd expect. One of Bobby's favourite tricks is beer with just a little bit of the stuff - if his visitor is human, they'll never even notice. If they're not, they burn.
Also, at one point, the boys assault a building full of demons by consecrating the sprinkler system.
The Newcomers in Alien Nation get acid-like burns from salt water.
This makes for an awesomeHeroic Sacrifice at the end of the movie, when Newcomer George sees his human partner fall into the ocean, and reaches into the water to grab him. In what other circumstances could you reach into acid and pull forth a (mostly) unharmed friend?
According to those involved in the later TV series, only the sea-salt mixture of SEAWATER had this effect. Salt water using ordinary table salt either had a much reduced or no effect.
The Newcomers also were kept in their ship for a long time and had built up a natural resistance, like how lungs adapt to higher-elevation living.
The demon Abaddon from The Secret Circle is killed when Diana's father drowns his host body, Nick, at the marina.
In one Flash Gordon story, a portal is opened to an alternate dimension populated with Mechanical Lifeforms. They prove hostile and nigh impossible to defeat, until scientists reveal their dimension is "completely dry" - spraying them with a firehose causes instant and lethal rusting.
Religion & Mythology
Many elements of European folklore have running water "washing away" magic. This has been incorporated into several fantasy series, and may be the reason vampires are said to be unable to cross running water under their own power.
The Wild Hunt could not cross running water. (Not that this often did much more than delay them. Depending on the myth, you generally needed to get cold iron or survive until dawn, as the hunt could travel to the ends of the earth in a single night, and could afford to take the long route.)
In Scottish folklore, an unlucky traveler might have to deal with a type of evil and disgustingsea-fey called a "nuckelavee" — a man-like creature that was merged into the back of a one-eyed horse from the waist down (kind of like a centaur, except the horse's head is there too). The best way to escape one of these skinlessabominations was to get fresh running water between it and you. Crossing a stream usually worked.
Possibly one of the more famous Scottish ones is "The Tale of Tam O'Shanter" who, after being discovered by witches has to cross the "keystone of the bridge" in order to escape. He makes it, but his horse gets her tail pulled off. I think the American version of this is Sleepy Hollow, with Ichabod Crane?
Ireland's Kelpie is a fey that takes on the guise of a black horse and kills people by taking them on a wild ride before drowning them, then eating their livers.
In Rifts, Vampires can be harmed, even killed by running water. This apparently means any water in motion. That means water hoses and squirt guns are effective weapons when vampires attack.
Warhammer fantasy role-play has a superstition that this is how you kill fire wizards. It doesn't work.
In Witch Girls Adventures, this is the biggest downside to having Hag's Syndrome. You can cover up the green hair and skin and red eyes with makeup and the like, but there's not much you can do about your tendency to melt when exposed to water, except avoid it.
Dungeons & Dragons allows you to do damage to undead by throwing bottles of holy water at them.
Final Fantasy VIII: the scarce Water magic spells (Water and Leviathan) are weak spots to a handful of enemies. However, fire-based foes are only weak to ice magic (Blizzard, Blizzara, Blizzaga, Shiva). Water is also useful early in the game when it is junctioned to offensive stats (Strength and Magic) as it dramatically boosts those stats compared with other offensive magic.
A notable example is the Alien Wily in Mega Man 2 whose only weakness is Bubble Lead, with every other special weapon actually healing the boss. The alien is really a hologram, so the water based weapon shorts out its hologram projector.
All the vampires in Legacy of Kain are hurt or killed by water, except for one clan in Soul Reaver that evolved a resistance to it, and Raziel once he acquires their power.
In Dominions 3, vampires and vampire lords cannot go underwater by any means. If they do end up in a water province somehow they are killed, permanently. Which can give a player a nice Palm Face moment if he's playing an aquatic nation and summons some vamps for their immortality, only to find out that vampires killed in battle do respawn... in their underwater capital.
Certain ghosts in Luigis Mansion can only be sucked up if you spray them with water first. Or, alternatively, just drench them until they fade away.
The Scarlet sisters, being vampires, are weak against running water. In fact, the backstory of the Extra Stage in Embodiment of Scarlet Devil had Patchoulli casting a rain spell to prevent Flandre from leaving the mansion.
The Endermen in Minecraft take damage from water, including rain. An easy way to kill an Enderman fast is to use a Water Bucket on it.
After the 1.9 update, Endermen have gotten around this weakness with Artificial Brilliance, any Endermen exposed to water or rain will immediately teleport away.
In Fallout 3, mirelurks (huge bipedal mutated crabs) in the Jefferson Memorial basin start dying once the purifier is turned on in Broken Steel. Apparently, mirelurks can only survive and nest in irradiated water and die upon prolonged contact with fresh water.
In the InFamous franchise, Cole dies from overexposure to water because it conducts the electricity within him, causing him to electrocute himself.
In The Firemen your fire hose and water grenades are your only means of defense against enemies, which makes sense as all enemies are fire, robots, or flaming robots.
Rain from Mortal Kombat weaponizes water. Originally, he could form it into a cohesive ball used in projectile attacks (which let him move his opponent around the arena, oddly), and then in the reboot, he gains a few additional moves with it, and it factors into both his fatalities.
Webcomics / Web Originals
In Sluggy Freelance, an army of robotic water coolers is defeated by knocking over their water tanks. Apparently Hereti-Corp never thought to waterproof their water coolers.
Averted in a crossover between The Wotch and Accidental Centaurs with, you guessed it, the wicked witch. No one ever thinks of using water against her. When it IS brought up Lenny points out that she's already used to it, so it wouldn't have worked anyway.
In Batman Beyond, water mixed into and diluted Inque's liquid body to the point of her being unable to hold herself together. This was used against her a few times, like her Batman: The Animated Series predecessor Clayface (though, being denser, it took a while for it to work on him.)
In Teen Titans, Beast Boy discovers that water is the most effective weapon against the Big Bad's army of mooks, which turns them into tofu. Cue epic super soaker gunplay!
Overload was also easily defeated with water at the beginning of "Car Trouble".
Also, in Teen Titans: Trouble in Tokyo, they captured Saico-Tek, who attacked their home; during interrogation, he set off the water sprinkler and disappeared. Beast Boy made a joke that he wasn't waterproof, that no one took seriously. It was later revealed that Saico-Tek, as well as the other colorful villains they faced during their visit to Tokyo, were made of ink, so he did pretty much get killed by water.
In Invader Zim, when Zim is hit by water he screams wildly and his skin gives off smoke/steam with a horrible sizzling noise. It is heavily implied that water acts as an acid to him, if it isn't said outright in the show, and so if Dib ever managed to pour enough water over him, he'd probably melt in a rather horrific fashion.
Except that, unlike the aliens from Signs, Zim quickly discovered a way to waterproof himself once he discovered the weakness, which was to bathe himself in glue.
In the third Barbie Fairytopia movie, one of the guardian fairies' apprentices, the fairy Sunburst's powers are weakened by water. When Laverna captures her and takes her place, Sunburst is left trapped inside an underwater bubble until Elina rescues her.
Kim Possible has a minor variation on this trope when Dr. Drakken creates an army of Kim clones. It's eventually discovered that the clones are susceptible to carbonated water, prompting Kim to unleash the awesome power of a soda fountain upon the clones.
Darkwing Duck villain Megavolt will short-circuit if splashed with water. Large amounts of liquid (such as Liquidator, a pure water being) effectively knock him out.
Liquidator himself knows several decent methods of killing it with water, ranging from boiling water to water hammer to a freaking tsunami. And when he collides with Megavolt...
For the most literal way to Kill It with Water, there's always drowning, a danger for all creatures unable to breathe underwater.
While not killing it with just any kind of water, you can kill a freshwater fish by throwing it in salt water, or a saltwater fish by throwing it in fresh water and watching osmosis happen.
Before people actually wish to try this, realise one thing: Osmosis is the process of salts and water creating a new balance within cells. Throwing a sea fish into fresh water will make all its cells rupture. His skin and organs will turn into slime. A fresh water fish thrown into salt water will die of dehydration. That's how badass osmosis is.
In the Yom Kippur War, the vaunted Israeli "Purple Line" was a series of sand fortifications that faced the Suez Canal. Because it essentially a gigantic wall of man-made sand dunes, it was considered extremely difficult to breach, especially for a force that would have to conduct an amphibious landing under fire beforehand. In a stroke of genius, the Egyptians blasted it apart with water cannons in under 30 minutes and sent their tanks through the gap, eliciting a Mass "Oh, Crap!" from the Israelis. (Egyptians sometimes cite this as part of their national myth of unorthodox ingenuity, calling it a "very Egyptian solution.")
Chinchilla fur is so thick that it cannot air-dry on its own. If a chinchilla gets wet and is not dried properly, the fur on top will dry and trap the moisture on the skin underneath. While this doesn't lead to death immediately, it opens the chinchilla up to fungus growth, fur rot, and other diseases.
Most electronic equipment will not survive long contact with water. Just how long varies.
There was the infamous case of a woman in the US who entered a contest named "Hold your wee for a Wii". The purpose was to drink lots of water and hold their urge to pee, but the lady drank too much she was poisoned with water.
In a pretty hilarious reference to this trope, a student called for a ban on dihydrogen monoxide as part of his science project—and got 43 students to favor the ban.
Banning "dihydrogen monoxide" has become a very popular petition any time and place there is an abundance of enthusiasm and a lack of information on scientific matters.
Related to the supernatural examples listed above, graveyards are often built next to a stream, and you can generally tell where the people it was built for lived by crossing over that running water. (iron fences are a secondary favorite)
If you go down too deep, that oxygen tank on your back won't do you any good. Water pressure will kill you. Water has weight, and enough of that weight can and will cause injury or death to anything unfortunate enough to be exposed. Except for inanimate objects, and only on the technicality that they're not alive and are thus damaged or destroyed instead.
The means by which pressure kills you isn't really obvious, though. If you multiply the surface area of the human body by atmospheric pressure, you'll find that the total atmospheric force exerted on a person is about 40,000 pounds. This doesn't hurt us a bit, though, because the pressure inside of us is the same as the pressure outside, so there's no net force acting on us. If I'm not mistaken, what kills you is the high amount of oxygen in your bloodstream. Likewise, if you put an unopened bottle of Pepsi at the bottom of the ocean, very little will happen to it, because Pepsi, being a liquid, is pretty much incompressible. The only thing that will happen is that the air bubble at the top will shrink.
Among the victims of the persecution and martyrdom of Japanese Christians in XVII century Japan, the Martyrs of Unzen were either drowned to death in the Shimabara river or, as mentioned in the Amakusa 1637 example, fatally scalded in the sulphur springs of Unzen.
More than one myth about Roman martyrs mentions them being tied to stones or anchors and then tossed into either the sea or rivers. Some of them are, however, very inaccurate; martyrs would NEVER be thrown in big rivers for practical reasons, and if the anchors were tied to their necks, the weight would've caused them to rip the victim's head off instead of pulling them down to the river's bottom.