Woodfall Swamp is covered in it, although after you beat the boss, it becomes unpolluted.
Great Bay has a variation, where the ocean has become warmer and grown murky, meaning that going too far off into it without a guide causes Link to become lost (it's also apparently killing the fish and is dangerous to the Zora).
Simon's Quest also has purple poisonous swamps that slow you down and eat away your life meter.
All the water in Castlevania 64 is poisonous, and literally dissolves the player like acid if (read: when) you fall in.
Ōkami. In Tsuta Ruins, there is a very obvious (purple!) lake of poison water. Amaterasu's Exposition Fairy prompts her to draw a lily pad on the water, which is instantly destroyed. Once you destroy the totems that are polluting the water, it immediately clears.
The same purple water appears in other places as a course hazard. If Ammy falls in she dies instantly, with a howl that will haunt your dreams.
Later on there's a Womb Level where you have to use lily pads to move across a river of stomach acid. The acid functions just like water except rather than costing you a unit of health if you stay in too long it damages your health directly.
American McGee's Alice didn't have instakill water, but in the early stream levels a fish would eat you if you stayed in the water for more than a few seconds.
Lego Star Wars II: In a Tatooine level in A New Hope, there is an area dotted with moisture vaporators that has deadly pools of mud. A vaporator next to it, when activated, can suck the area dry and provide a walkable surface.
Lego Batman: there is regular water which is quite swimmable and of course grimy water with will kill you instantly. The bad water is actually green toxic waste and is accessible when you have unlocked certain characters that are immune to the toxins.
The purple water in the first act of Act Raiser's Bloodpool causes instant death, needless to say.
MediEvil gives us an entire level based around this known as the Pools of the Ancient Dead. While Sir Dan has Super Drowning Skills and will lose a life bottle upon touching water anyway, (being dead doesn't exactly do water for one's buoyancy, you know!) the entire level here is absolutely covered in this and falling in is all too easy thanks to the landscape and all of the exploding chests that, while they don't damage you outright, will do one worse and send you flying into the water.
TR2 had green in one level and red in another. The red water was meant to be lava, despite it being... well, red water. Made worse by the fact that a) when you fell in it, you stood up and then keeled over and b) the very next level had proper instant burst-into-flames lava straight from the original TR.
TR3 had an annoying and possibly terrifying variant, quicksand. Lara sank very quickly unless it was a designated shallow spot, once submerged your breath meter went down very quickly, and the kicker? Lara was unable to climb out of the stuff.
Also, falling into regular water on a vehicle resulted in it exploding.
Once again in TR3, the penultimate level had stuff that... well, it sure didn't look like lava. More like bright gold paint. More like molten gold, given its effect on you.
Hell, even normal water wasn't safe from this Nintendo Hard masterpiece. Some ponds had Piranhas in it, which despite not working that way, would butcher Lara in less than three seconds if she was caught in a school of the stuff.
Don't forget the subzero arctic waters in the end of the game. While you can swim in it, the hazardous cold water is only survivable for a few seconds. Once your exposure meter is depleted, then your health drains fairly quickly. If you dive under the water, the meters drain even faster.
Underworld has glowing blue (radioactive?) water in its final levels. Instant death if you so much as touch it.
This would be eitr, appropriate given the setting, and yes it is that deadly.
The first and last boss arenas in TR3 also have "fire water" that kills you if you touch it.
Evolva: Not the river water that appears in most levels, but the sea water that appears in levels 9 and 10. It drains life quite fast if you merely touch it, and diving into it causes instant death (in contrast to lava, which takes a few seconds to kill you). Oh, and the shield skill doesn't you protect you from it.
King's Quest VI has a section with instant death water - entirely justified given the fact that it's in the Land of the Dead, and said death water is the water from the River Styx. King's Quest: Mask of Eternity also has instant death water in the Dimension of Death, along with harmful pools of blood in the same Dimension, plus toxic water from the Swamp (some of which is covering a small pond in Daventry). King's Quest II also had the swamp and lake surrounding the vampire's castle. Instant death for Graham if he swims it, so he has to find a way to hitch a ride.
The Half-Life series has health-point-draining scummy green radioactive contaminated water. It is your HEV Suit that lets you survive contact as long as you get out fast. Radioactive waste is sometimes replaced with identical-looking biowaste. The difference is that while radioactive stuff triggers the Geiger counter and it does damage while you stand in it, biowaste has no audio warning and continues damaging for a while even after you leave it (and this damage is subtracted directly from your health, ignoring all armor). And of course there are the respective trefoil/biohazard signs on your HUD while you are being damaged. There is also an inversion — the healing puddles of goo on Xen.
Quake has both toxic waste and lava (which still behaves like water), as well as clear (and murky, but harmless) water.
In Turok 2: Seeds of Evil, the River of Souls (which is both its own level, an extends through a couple others) is legendary for deadly properties: anything that drinks from or falls in the water dies instantly. Towards the end of the game, you find out the river is polluted by discharge from the Big Bad's spaceship, and you are tasked with purifying it towards the end.
While green nukage and lava are always harmful in Doom and the extremely blue water is always harmless (the exception being a lonely, conveniently marked as toxic, blue water pool in Doom 1's Episode 3, level 3) , whether or not brown slime and blood are damaging varies depending on the whim of the level designer. Every so often a custom wad designer will be a really big asshole and make blue water dangerous, due to being radioactive coolant water for a reactor, electrified, or freezing cold, or, in an inversion, make what looks like nukage harmless (as just green water, most likely), a common sighting in the Plutonia megawad.
Duke Nukem 3D has puddles of radioactive waste that can be made walkable with a pair of special boots. Most of it isn't deep enough to be submerged, let alone swim. Strangely, if Duke dives into pools of waste that are deep enough, he loses oxygen (as if he is in water) instead of health.
Almost all bodies of liquid in Unreal Tournament either instantly kill players as soon as they fall in, or slowly damage them for as long as they're submerged. In some cases this is justified (lava in CTF-LavaGiant), in others not so much (the water in DM-KGalleon).
Three examples in Conduit 2. There's a small but lethal pool of glowing blue...stuff in the first level that is otherwise mostly for show. The levels in Atlantis have electrified water that is instantly fatal. And lastly, the China level has this quicksilver-like liquid that will also kill Mr. Ford on contact.
In addition to lava pits like in the first two games, Descent 3 has green acid/nukage that also damages your ship.
Doom has an early example of this, blue water on the floor was perfectly fine but anything green was toxic and would deal damage unless you picked up a suit power-up.
In The Lord of the Rings Online, up in the frozen lands of Fornost, going into the water instantly causes death, perhaps due to freezing. You can enter other water just fine, it's just the water in the arctic type area that is deadly. In the same game, Angmar has bright green water that is instantly fatal.
Guild Wars, where some water (mostly in Kryta, and then more often in Factions' Undercity) inflicts poison on you. Walking in actual sewer water (which is a dull bronze color), strangely, usually has no effect.
In World of Warcraft, swimming in green water such as the kind found in Undercity and Scourge ziggurats used to cause damage overtime, though rather minor and very easy to get out of. As of Cataclysm it no longers does this, while the equivalent in the Naxxramas raid dungeon still does- the latter will likely take off half your health or more unless you execute a perfectly timed jump over it.
In FusionFall, large green pools of "Fusion Matter" lurk in many of the regular and infected areas. Swimming in, walking through, and even sometimes walking NEAR these pools causes the player to take damage.
In Metroid/Zero Mission and Super Metroid, the "water" in Brinstar was highly acidic and would damage you until you got out. The Varia upgrade removed the hazard.
In Super Metroid, there is no suit which protects you from acid. The Gravity Suit prevents you taking damage from Norfair's lava, but the acid is still a problem. In Zero Mission, the acid in Brinstar becomes safe to travel through with the Varia Suit, the lava in Norfair is safe with the Gravity Suit, and the acid in Tourian is never safe.
Justified in the first two Metroid Primes: In the first, one of the first bosses was filling the water with toxins, and when it was defeated the water stopped causing damage. In the second the water was in Dark Aether, where pretty much everything is lethal.
Metroid II didn't even make a pretense of calling the fluid on SR388 water; it was acidic, toxic and generally lethal. The only way to remove the hazard was to drain the stuff.
In Metroid: Fusion, Sector 4 AQA featured electrified water, which would cause continual damage if you fell in. Draining the water removed the hazard.
Whenever you encounter water that's an odd colour in the Banjo-Kazooie series, there's often something living in it, namely piranhas in the first game and Dragundas in Tooie. Strangely, it seems the only reason why the polluted goo is dangerous is because of the Dragundas who live in it, not because it's toxic.
Gobi Desert includes untouchable sand, dangerous not because it would suck you in but because it includes irritable sand eels.
Seems like a favorite trick of the programmers at Rare; they did that in the Donkey Kong Country series as well.
Rusty Bucket Bay has a variation: Banjo can swim in the polluted water, but the oxygen meter depletes even while swimming on the surface and twice as quickly underwater.
Speaking of Rusty Bucket Bay, there is a small area on land that is full of glowing green waste and toxic barrels. Contact with the waste is not instant death but it damages instead. Similar technicolor goop is found in Grunty Industries in Tooie; maybe that's where all the toxic waste came from.
The freezing water in Click Clock Wood winter uses the same mechanic as the oily water in Rusty Bucket Bay. The water in Freezeezy Peak just mocks you while it drains your health.
Mad Monster Mansion includes what could best be described as a pool full of haunted water (the game does not explain why the purplish liquid harms you). Oddly, you are protected from this damage if you're an adorable pumpkin.
That is because harmful terrain doesn't affect you if you are transformed. Usually justified in that the form you take isn't bothered by the terrain (e.g. crocodile-form not bothered by piranhas). The hidden Washine Machine transformation is immune to all such terrain, since the Transformed flag is set.
Even otherwise clean seawater is a hazard to poor Banjo. Swimming in the sea in Treasure Trove Cove attracts the attention of an enormous frickin' shark that seems to be stalking you.
Notable exception: Swimming in the waste water in Clanker's Cavern (or even inside Clanker) is no more hazardous than 'normal' water.
Donkey Kong Country 3 puts a twist on the formula with toxic water with no effect other than the player's directional pad is reversed, so you must press left to swim right.
Super Mario Sunshine has Noki Bay, where the otherwise crystal-clear water is horribly polluted from an eel in desperate need of a dentist. Only the surface is harmful, and since several of the levels there give you a suit that lets you stay underwater longer, it's actually safer to just swim under the water when you have to go in.
There was also Ricco Harbor before it, where Gooper Blooper polluted some of the water with his ink. In both of these cases, the water literally deals a hit a second, barely giving you any time to either jump out or dive down lest you get stuck.
Before that the lake in Bianco Hills was polluted for two chapters.
Super Mario Galaxy had a level or two where the water or some other substance was so toxic that falling into it resulted in instant death as the player watched Mario stick his hand out and garble under the muck before drowning.
Both the original game and the sequel had pools of dark matter which cause Mario to disintegrate upon making contact with them.
And then, in Super Mario 64, the second ice world you come to has two types of water, both harmful: one is swimmable, but because of the freeziness of it, it slowly drains your life rather than help you to replenish it. The other is cold enough to act exactly like lava and forms the backdrop of a boss battle.
Said "death water" was also present in some levels of the original game, particularly the fortress levels.
Super Mario 3D Land has at least one underground level with boiling purple sludge that kills Mario on contact in a manner similar to lava, only with purple smoke burning Mario's rear instead of fire.
Paper Mario: Sticker Star has World 3, a forest that's covered in dark purple poison, which damages Mario when he steps in it and randomly hurts him if he enters battle in it. The poison vanishes after the world's boss is defeated.
In Ratchet & Clank games, clear water is safe to swim in. Murky water always contains Lombax-eating fish.
In the first game, an obstacle course level had pools of clear water with those very fish. You usually had to drain the water and kill the fish, then fill it back up or they would eat you. Also, freezing cold water will instantly freeze Ratchet to death, and the poor furry guy can't swim in mud or poison goo, he simply sinks.
Pleasantly, the clear water pools at least had visible fish.
Strangely enough, Ratchet is capable of jumping out of the opaque goo in almost every level of the first and second games in the series, but will drown if he falls back in three times. In Up Your Arsenal, it kills him instantly.
Exploited in the Gemlik Base level of the first game, where in the section where you walk on the left side of the room, the rising orange liquid will cause Ratchet to fall off of the path.
Played with in Going Commando in that the main path in Notak ended in a puzzle where you had to freeze and thaw the fish-filled water to progress.
Appears again in the Obani Draco level of Up Your Arsenal. Instead of causing Ratchet to fall off, it simply caused him to somehow enter his sinking animation despite not being in the goo before respawning.
The Rayman series does this as well. However, in those games, it seems as if the only thing that separates "swimmable" water from the "piranha-infested" kind is the presence of a sign...
Starting with Revolution, you could see fish jumping out. But only near walkable regions, so they could drop on your head and bite you.
Water in Rayman Origins is sometimes unsafe to be in for more than a second because it's infested with Darktoons or piranhas.
The Spyro the Dragon series, at least the Insomniac-produced ones, occasionally had this. One level in the second game had green water that you could walk on while using the invincibility power-up.
Played absolutely dead straight with the Dark Eco pools, however, which kill you stone dead.
Also played straight with the electrified water in Lost Precursor City from the first game (though it damages instead of killing instantly), which bears an unnaturally bright green hue and has odd yellow lines occasionally showing up.
The "Mega Mack" from the Chemical Plant Zone in Sonic the Hedgehog 2 (16-bit) doesn't kill you on impact, but it does cut the time you can remain in it before you drown in half, and is even more hazardous because unlike regular water, there aren't any air bubbles for Sonic or Tails to use to replenish their air supply.
Jett Rocket has two variations of this. The water in the first world is safe swimming. In the second world, the water is freezing, and while you can swim in it, it saps your rather limited health very quickly. In the third world, it will suck you into it and make you lose health, but you can wade through it for a little bit before this happens.
Croc: Legend Of The Gobbos has icy water that you can't swim in, as well as lava. However you can swim in certain areas of light blue water, which is necessary to rescue certain Gobbos.
In Epic Mickey, all bodies of water have been replaced by paint thinner, which damages Mickey upon contact (as he is made of paint like everyone else) and forces a small leap up. He has no Mercy Invincibility, and the hops are quick, so if Mickey gets tossed out too far, it's certain death. There are also 2D stages based on Mickey's past cartoons. Normal water exists in some of these stages, but Mickey reacts to them the same way he does to thinner.
Super Mario Fusion Revival has World 4-HC2: Poison Aqueduct. The level is a stealthy entrance into Hellfire Citadel itself by forging a path through its aqueducts. However, the aqueducts are filled with toxic liquids.
Portal has grimy instant death water. It is assumed to be highly toxic sludge, and falling into it results in an unsatisfactory mark on your official testing record, followed by death. In the sequel, it is presumed to be either highly toxic or highly acidic since one sign shows a drawing of a person whose lower body is disintegrated under the surface of the liquid.
In the first game this may be less to do with the quality of the water, and more down to the presence of the Aperture Science Handheld Portal Device. "Do not submerge the device in liquid, even partially." In the abandoned test chambers in the second game, it's more likely because the water has been sitting in a pure asbestos tank at the bottom of a polluted salt mine for about three hundred years.
Probably just the pollution. Asbestos isn't dangerous if you drink it, only if you breath the fibers for a few years. Of course if you do that you will get cancer, which is hardly an instant death. (Although many might wish otherwise)
All the water in Fallout 3 is irradiated, save for a very few places. You can still swim and drink from it, but will need to deal with the ensuing radiation poisoning afterwards.
If you have Broken Steel and released the Modified FEV into the water, the virus-laced Aqua Pura will adversely affect your stats and ultimately kill you if you consume a certain amount.
The Monongahela River in The Pitt has the most irradiated water in the game, with up to 600 rad/sec. Swimming here is a death wish.
Fallout Tactics is much worse, the water are obviously irradiated and glows with ominous sickly green glow.
New Vegas reverses the trend, in that (on top of the expected "clean" and "dangerous" types) there's somewhat natural looking silt-tinged water that's completely safe to drink, and absolutely pure and clean looking water that's absolutely lousy with radiation. The only real way to tell is to stop and wait to see if your Geiger counter starts clicking before taking a drink/hopping in.
Bahamut Lagoon has "poison swamps". They can be turned into regular swamps by casting healing magic on them.
This is the whole MacGuffin plot of the SNES RPG, Lagoon.
In Demon's Souls, the second stage of The Valley of Defilement is covered with this. Not only is the player unable to dodge when walking through it, but extended exposure causes poison.
In Dragon Quest VIII, there are a few areas (such as a segment in the Black Citadel) where the player can walk through what appears to be purple water. Doing so slowly damages the entire party.
Poisonous swamps appear throughout the series, but the only game where you can actually die from its damage is the very first one; sequential titles will never let your party's health fall below 1HP.
This feature is useful in the ninth game as there is a side quest which requires you to heal allies from exactly 1 HP several times... good luck getting monsters to drop you to exactly 1 HP, unless you have a lot of Defense and a lot of patience!
The Blood Priest in Wasteland is found in the middle of a lake of blood. The water doesn't hurt you (if you can swim)...but the fish do.
In Xenoblade Chronicles, the aptly named Poison Swamp in Satorl Marsh damages anyone who wades through its sickly purple water, but only by about 4% of their max HP every few seconds. The offcolored water at the Fallen Arm and Mechonis Field causes a significantly larger amount of damage, despite not looking nearly as dangerous as the swamp, though it mostly exists to keep you from swimming too far out into the ocean and to punish you for falling. Lastly, the glowing green pools of liquid ether inside the Bionis look dangerous, and will kill you very quickly; a fact one of the bosses tries to exploit by knocking your characters around and inflicting them with status effects that cause them run around uncontrollably or keep them from moving.
EarthBound also has a poisonous swamp that slowly damages anyone walking through. Except this one's called Deep Darkness and the water is murky.
Similarly, swampland in Final Fantasy Tactics is harmful, and any units that finish their turn while standing in the water will be Poisoned (treading water and climbing out onto solid ground has no ill effects.)
Swamp tiles in Fire Emblem Gaiden are often quite vast in the few maps they appear in, and they harm units standing on it for about 3~5HP of damage every time their army's phase begins while standing on it, swamp tiles also have a high movement cost (how many move points it takes to traverse it; the higher the value, the shorter distance that unit can go on that terrain), which makes it quite time-consuming(and unsafe) for a ground unit to cross.
In Grand Theft Auto III, the water surrounding the city is extremely polluted, to the point where it takes on a thick slimy dark texture, and a very dark blue color. The reason for this is supposedly industrial pollutants mixed with a massive oil-spill, thus creating water so grimy, it's fatal to anyone who tries to swim in it.
Likewise, in Grand Theft Auto: Vice City, the water is crystal clear and appears clean and safe, however attempting a swim will still kill you. Though it's never explicitly stated why, inspection of the Lifeguard Booths on the beach reveal a sign reading "Warning: Rip Tides", implying that strong rip currents are at fault.
Or the PC himself can't swim (as it is possible to swim in the prequel Grand Theft Auto: Vice City Stories). Also a subversion in some places - there are "pools", which are just typical pits with a water surface drawn over them from a graphical standpoint. They contain no actual water - beachballs do stay above the drawn water level, but the PC can can just jump in and doesn't experience any water effects at all. One of the "pools" is deep enough to let the PC be fully submerged after crouching - and no drowning occurs, no matter how long he stays there.
All There in the Manual, the water is supposedly filled to the brim with deadly ravenous sharks that attacks anything that enters the water deep enough.
In the later SimCity games, severely polluted water is brown.
In Second Life's Linden Realms, there is pale green and purple water that will send you to the nearest respawn point if you fall in.
A rare TV show example, MXC, the comically re-dubbed version of Takeshi's Castle, often features a muddy brown water that many contestants fall into in the various challenges. The water is given a disgusting name, every time it appears, like "septic sludge" or "toilet flushings from the Air Force One", often depending on who the contestants are.
The original Takeshi's Castle with the Craig Charles narration claims that this is runoff from a nearby pig farm in southern Japan.
Land of Wind and Shade in Homestuck has oceans of oil, polluted by the its denizen Typheus. John apparantly avoids entering it at all costs (and walkarounds treat it like walls), but then again most characters in that comic generally avoid going into any deep body of liquid.