Logical Weakness

Some authors hold that their character's powers shouldn't run exclusively on the Rule of Cool, and decide to inject some (relative) realism into the situation, resulting in a hero whose weakness is a bit different from the rest of the Super crowd.

These guys aren't allergic to arbitrarily chosen household items, nor strange items related to their origin story. Their weaknesses are, in fact, a direct result of their particular superpowers. For example, a character who can summon fireballs may find themselves powerless during a rainstorm (or a Shock and Awe hero might find themselves at risk of electrocuting themselves in the rain). Sometimes this can stem from a lack of Required Secondary Powers, like a hero with Super Speed but not Super Reflexes finding themselves going Too Fast to Stop.

Whatever the case, this type of superpower-induced weakness can function as a Drama Preserving Handicap, or it can be Played for Laughs. It may also create Elemental Rock Paper Scissors between different heroes.

Not related to the Puff of Logic. May be an aversion of Required Secondary Powers.

Anime and Manga

 * Naruto's Rasen-Shuriken attack is essentially a flechette bomb that attacks organisms' individual cells. It has a tendency to do this to the person who is holding it as well as the target.
 * One Piece Devil Fruits can frequently fall into this. Examples include Luffy's rubber body, which makes him more or less immune to blunt force but renders him no less vulnerable to blades than he ever was. Sir Crocodile's ability to turn into sand can be hampered by becoming wet. God Eneru's lightning-based powers had no effect on rubber, thus allowing Luffy to harm him.
 * A better example for Luffy would be that heat apparently makes him extra squishy.
 * Magma beats fire, which would probably beat ice. And for an odd example, the more or less completely useless by this point Mr. 3's wax power in fact blocks almost every single poison Magellan has.
 * Hikaru is created to be super fast and agile. The problem is that because she is so light, she doesn't have very much strength. She's also unable to fight well on places like an ice field.
 * In Fullmetal Alchemist, the fact that Roy Mustang is useless when it's raining is something of a Running Gag. This is because, well, he uses fire, and rain is going to put a bit of a damper on his ability to get a flame going. However, this is only when he himself (specifically his hands) are wet, because if something else is covered in water he can just decompose it into hydrogen and oxygen then ignite that.
 * In Brotherhood, Pride's Living Shadow powers don't work in total darkness since he needs a light source to cast a shadow.
 * Darker Than Black loves this. The guy with electricity powers needs something that conducts electricity if he wants to attack at a distance, the guy who can freeze stuff needs water (or your arm) within reach to be able to do anything, and in the first episode of the second season, someone with Super Speed who tries to run in a rainstorm winds up riddled with holes due to elementary physics.
 * Medaka Box loves this trope. The best example is probably the array of weaknesses that Yukuhashi Mizou's abnormality, mind-scanning, has, thanks to it working really, really good.
 * Many of the Clow Cards from Cardcaptor Sakura have logical weaknesses. One example: Sakura managed to capture the Watery card by trapping it in an industrial-sized freezer.
 * In Mahou Sensei Negima by turning into lightning. This is countered by Rakan pointing out that lightning gives off positive streamers at the destination meaning he knows where it's going to strike. And because his perception isn't speeded up as well he can't properly control himself.
 * Keima, the main character of The World God Only Knows is a legendarily skilled player of Dating Sims in which one pursues girls. However, the opposite of this (girls pursuing him) frequently leaves him at a loss.
 * Magical Record Lyrical Nanoha FORCE introduces the Huckebein family, carriers of the Eclipse virus which grants them ridiculously powerfull Anti Magic abilities among other things. by themselves they're pretty strong but for most or them the only reason they can fight against the obliterating magical powers of the main cast. Lampshaded mercilessly with the fight of Signum Vs. Cypha where the latter was receiving a sound beating until she activated her full Anti Magic hax.
 * In Mirai Nikki, police detective Keigo Kurusu's future diary feeds him data from whatever investigation he's currently conducting. The solution?
 * Accelerator from To Aru Majutsu no Index is practically invincible due to his power--changing any vector he wants. He can easily deflect bullets, kill someone by reversing their bloodflow, turn air into plasma bombs, et cetera. However, much like Firestorm in the Comics section below, he has to actually mentally perform all the relevant calculations to do any of this. all but cripples his abilities.

Comic Books

 * In Runaways Victor is a cyborg and can't pass through metal detectors without setting them off.
 * Plastic Man, because of his rubber based powers, is been known for having a vulnerability with extreme temperature changes and (in some incarnations) being in contact with acetone.
 * Wolverine of X Men can't pass through metal detectors because of his skeleton. He is also vulnerable to magnets.
 * Of course, this doesn't stop him in any story that requires him to travel by plane. At least once this has been played for laughs, with Wolverine and another character walking out of an airport while she comments on how she's always wondered how he got through metal detectors and now she knows. The reader, of course, is not privy to this information.
 * Once, he walked into the Pentagon, and showed a medical certificate stating he has metallic prosthesis due to war injuries. Not far from the truth.
 * In the Ultimate Universe, he once got in by sticking a (fake) grenade into some guy's bag so airport security would freak out and he could sneak past the detectors in all the confusion... Ultimate Wolverine is a bit more of a Jerkass than regular Wolverine.
 * Humorous example verging on a Weaksauce Weakness: the Sandman was first defeated when Spider Man vacuumed him up.
 * He also once teamed up with Hydro-Man, until they realized that if they touched, they combined into a sort of sludge.
 * Static can't use his powers in direct combat (electricity doesn't jump air gaps normally) in the comics as well as he can use them to make the area work for him. A bit of an odd example, his weakness actually forces him to think around his powers and often coming up with mundane solutions as often as ones that use his powers.
 * Shadowcat of the X Men can only stay phased inside an object as long as she can hold her breath. 'Cause, you know, there's no air inside solid objects. (When the character debuted, it was pretty clear that she couldn't breathe at all while phased, which made sense because air, while not solid, would still be out-of-phase relative to Kitty. It was invoked for story reasons, to make the character sometimes vulnerable when in costume. It changed to its current interpretation around the time of the Mutant Massacre, when she got injured and her default state became "phased". If she couldn't breathe while phased, this would have killed her quickly.)
 * Colossus of the X-Men can turn himself into organic steel completely, including all the internal workings of his body. Apparently he does not have blood in this form (and neither does it require it). One downside to this is that if something does manage to injure him through the Nigh Invulnerable status, turning back into the more frail and bleeding human form would be a Very Bad Idea. Fortunately he can still heal with time. In his metal form, the equivalent of setting broken bones requires heavy machinery.
 * Firestorm's main power is transmuting matter. He can change practically anything into practically anything else, such as lead into gold, or air into gold, or bullets into water, or water into plutonium. Not even considering his additional powers, this would make him nigh-godlike, except for a Logical Weakness: he has a normal human mind and no Super Senses, so he needs to mentally keep track of the chemical composition of everything he transmutes. This means that he can transmute things freely into elements and very simple compounds (like water (H2O) or salt (NaCl), and maybe even TNT (C6H2(NO2)3CH3) at most), but making things more complicated than that requires great concentration, if he can do it at all.
 * Having witnessed the fiery deaths of his family, along with the rest of his species, the Martian Manhunter now suffers from pyrophobia. (The pyrophobia of the other Martians is handwaved as being a psychic block implanted by the Guardians of the Universe to stop them becoming too evil or something, but with J'onn it makes sense.)
 * While not his most prominent weakness, Superman is at least hurt by high powered sonics. His super senses and invulnerability seem to roughly cancel each other out in this instance.

Film

 * Violet in The Incredibles can be seen while invisible if you throw something other than her suit on her. It has to be her custom-made supersuit too. Her regular clothes stay visible when she vanishes.
 * Frozone, also from The Incredibles, relies on the water in the air to use his ice powers. When he's in a place with no water, like an apartment fire, he's useless.
 * In Unbreakable David Dunn  has the realistic weakness of water. This makes sense, as water wouldn't be affected by  . Also a bit of Fridge Brilliance when you remember that he nearly drowned as a child. This takes it from being a physical weakness, to being a mental weakness as well in the form of a phobia. There's a lot you can do to get around being able to drown. It's a lot harder to get around a crippling fear of the water.

Literature

 * In the Wild Cards books, Philip "Fadeout" Cunningham can turn invisible, but he can't see if unless his eyes are visible (as, like anyone, his vision depends on light contacting pigment molecules in his retinas). Fortunately (for him) he can turn parts of himself invisible while leaving others opaque, so he counts on the fact that a pair of floating eyes are hard to spot at a distance, especially in dimly lit areas (plus, he can always make his eyes vanish if hiding is more important than seeing his surroundings).
 * In Codex Alera furycrafters that work with one element can be disabled through relatively simple means. Aircrafters are covered in dirt, earthcrafters are suspended off the ground, watercrafters are dehydrated, firecrafters are placed in small spaces (so any fire cooks them alive), and wood/metal crafters are stripped of their respective elements. Disabling someone with multiple elements is trickier, but doable.
 * The Vord Queen specializes in these, to the point where at any point where her enemies seem to be winning, she improvises (or already planned) a solution that nullifies her foes' advantage. At one point, when  goes full-on Chrome Champion on her, she figures out a rather simple weakness, and coats him in ice, making the metal that makes up his skin extremely brittle and excruciatingly painful.
 * One of the main limitations on magic in the Dresden Files (or, rather, the mortal magic, as werewolves and faeries seem to sidestep the issue) is that you really have to know what you're doing for something to work. You can't transform someone into a frog without knowing an awful lot about the anatomy of frogs... and if you don't want to destroy someone's mind in the process you have to really know neurosciences. So, essentially, it's impossible. Also banned because it's so dangerous.
 * Not sidestep so much as displace; weres get help (through bargain, artifact or rituals of communion) from something which does know all of that, and some nonhumans such as certain faeries fall into that category. Their minds and senses simply give them complete and accurate knowledge of all of the details of the relevant natural processes; for them extrapolating from a strand of DNA to a creature's adult form, natural environment and group dynamics may be as simple as pluralizing a word... and requires no greater intelligence than the latter feat would for a human. This actually carries its own Logical Weakness in that a being that aware of cause and effect is at base restricted by that awareness.
 * The Mistborn series follows a very strong Magic a Is Magic A system, so many powers can potentially be a double-edged sword. Someone burning tin (which gives Super Senses) can be incapacitated with loud noises or flashes of light, for example, and to be any good as a Coinshot (telekinetic control of metals), you'd better have a really good understanding of elementary physics- try and Push something bigger than you are and you'll be the one flying across the room instead.

Live Action TV

 * Will and Watson found Clara when she was invisible by turning on the sprinklers to get an outline.
 * The Sarah Connor Chronicles reveals that Terminators can't swim. It also reveals that they can be temporarily disabled by powerful electrical shocks, although they reboot themselves in a couple minutes. Also, they set off metal detectors.
 * From Heroes:
 * Elle Bishop generates electrical blasts. However, her electrical powers are usually focused outwards, and she's not insulated from her own blasts. So if she's coated in water and attempts to use her powers, she just ends up shocking herself.
 * Claude, an invisible man, still has a heat signature and is thus able to be seen with infrared goggles.
 * As an aside, Noah Bennet presumably has an entire manual full of these.
 * Matt Parkman, due to his telepathy, is somewhat more vulnerable to bright lights and loud sounds while using it. This makes sense, as he's not just hearing the sounds/seeing the flashing lights with his own senses, but also the senses of the people whose minds he is reading and thus his brain can't handle it all at once.
 * Noah Bennet shields his thoughts from this by thinking in japanese, a language Matt can't understand.
 * In Star Trek the Next Generation, Data, the android, has the standard weakness to electricity and electromagnetic radiation. He's also too dense to float or swim, although he can survive underwater.
 * Although in the event of a water landing, he's designed to operate as a flotation device.
 * Maybe he has an airbag that he can inflate but is potentially damageable.
 * In an episode of The X Files, a Literal Genie grants someone the power to become invisible. He has to strip naked to make any use of it, which he considers a small tradeoff, although it makes going outside uncomfortable. Even more uncomfortable: he promptly gets hit by a car because the driver didn't see him. A previous "beneficiary" of the genie's wishes ended up with an inhumanly large, ahem, manhood. He then keeled over from lack of blood to the brain when he got excited. And the paramedics trouble getting him through the door while he was lying on his back.
 * In "Trevor," the titular con gains the ability to become intangible after being struck by lightning. While he has the ability to pass through conductive objects, destroying them in the process, he's powerless against non-conductive materials. He's eventually killed when struck by a car - he can phase through the hood, but not the windshield.
 * An antagonist in Angel had the ability of Detachment Combat. He couldn't stay separated for too long or his parts would suffer necrosis from the lack of nutrients.
 * In Alphas it's pretty well established that with every alpha ability comes a weakness of some sort. In early episodes, the most notable was Rachel, who has hyper, sentinel-esque senses. She was initially shown to be able to enhance one sense at a time, but while she did so, she couldn't use her other senses. (While her vision or smell was enhanced, she could not hear the other characters when they spoke to her.) This is a great weakness, which makes all kinds of sense. However, the writers seem to be forgetting about this weakness, as in recent episodes, she's been using her abilities without shutting the rest down.
 * In The Lost Room many of the Objects have amazing abilities but also have serious weaknesses
 * The Key can let you enter and leave the Room through any door anywhere in the world (and thus lets you travel almost everywhere) but it cannot be a sliding door and in order to open the door it needs a tumbler lock. If you not careful, you can trap yourself.
 * If you touch the Ticket you will be teleported just outside Gallop, New Mexico no matter where in the world you are. It's very handy for quick getaways and to dispose of attacker or people who simply annoy you. However, its owner kept teleporting himself to New Mexico whenever he handled it. He finally was able to cover enough of it in duct tape that he could handle it safely.
 * The Comb allows you to stop time for ten seconds but when the effect ends you need to be perfectly still or you will suffer terrible motion sickness. The short duration of the effect means that you might have to use it repeatedly and your body will suffer the consequences.

Tabletop RPG

 * Some of the Disadvantages of characters in the "Champions" superhero RPG were of this type. For example, the insect-like alien Insectoid took damage from exposure to the insecticide malathion.
 * In both Vampire: The Masquerade and ''Vampire: The Requiem, characters can buy a power that allows them to heighten and refine their senses. Of course, if there's a sudden change in sensory input (e.g., opening a storage locker to find a rotting corpse when you've got heightened smell up), you're probably going to be reeling.

Video Games

 * Cole McGrath from In Famous is officially the first protagonist of a sandbox game that can justify his inability to swim. (In fact, he IS able to swim for a very short while, and he's perfectly fine if he steps in a small puddle, although if someone else steps in the puddle shortly afterwards they won't be so fine.)
 * Chain-link fences provide perfect cover from Cole's lightning for the same reason - electricity, by its very nature, follows the path of least resistance and gets grounded by those fences.
 * Alex Mercer of Prototype, due to the way his offensive and defensive abilties are set up, and the fact that he absorbs people and thus incorporates their mass into his own, is literally too dense to swim. This is apparently true of  Though he can jump off the bottom of the East River because he sinks nearly as fast as he falls.
 * But then again this applies to everything in the game, infected or not. Anything not capable of jumping like that dies instantly on contact with water.
 * However, despite his immense mass he can still fly by shooting blood out of his hands.
 * It's not so much flying as gliding, although that does not excuse the incredibly long distances he can do it.
 * The Mega Man games often use this: Electric guys experience shorts when you stick a blade in them; fast guys are vulnerable to time stopping, and so forth. The Weapon Archive in 10 is a Puzzle Boss/Final Exam Boss that requires you to know your Mega Man history and ask "Which of my weapons is most like what beat this guy the first time?"
 * Mega Man 8 has these for six out of eight Robot Masters. Clown Man gets tangled in his ridiculously-long arms if hit with Tornado Hold; Thunder Claw is the only safe way to bounce Grenade Man's bombs at him; Sword Man (who's fire-based) is left smoldering if hit with Aqua Balloon; Search Man lights on fire if you hit his bush hiding spot with Flame Sword; Astro Man, a neurotic (listen to his greeting), freaks out and can't move if you lock on with Search Missiles; and Tengu Man, a flying boss, is grounded by the Ice Wave (like how airplanes are grounded if their wings ice up). The exceptions are Aqua Man (weak to the Astro Crush) and Frost Man (blinded by the Flash Bomb, which doesn't have an obvious logicistic given he's An Ice Person).
 * In some cases, though, it requires some advance knowledge of the boss to be able to figure out what to use. In the tenth game, why would Strike Man's weapon be the best to use against Sheep Man? Because the former uses the Strike Rebounder (which bounces around due to being a rubber ball) and the latter uses the Thunder Wool. In fact, while every boss in Mega Man 10 has weaknesses that fall into this trope, most require knowing just what the boss does.
 * Likewise, Mega Man X also uses this. Ice bosses like Chill Penguin, Frost Walrus, and Blizzard Wolfang can't stand fire (fire melts ice), while Fire bosses like Flame Mammoth, Magma Dragoon, and Burn Dinorex are weak to wind (wind blows out fire).
 * Similar to the above examples, John Marston from Red Dead Redemption can't swim. It makes sense since the charater has spent most of his life in the Wild West, where there isn't a whole lot of water. The above ground water sources we do see are mostly fast moving rivers or dirty and swampy. Also the game takes place in 1911 and most people couldn't swim back then.
 * Much of Pokémon's Elemental Rock Paper Scissors falls into this. For instance, electrical attacks are stronger against Water- and Flying-types because they conduct electricity. Meanwhile, Ground-type Pokémon, being always grounded, are immune.
 * Even if they're part Flying-type...
 * In Magicka, while your characters are all Squishy Wizards already, you can shock yourself if you use electricity while soiaked.
 * A stone based monster in Final Fantasy IX can be killed instantly by using a Soft on it, which is normally used on petrified allies. The game states that the monster "became too soft to live".

Web Comics

 * In the Ciem Webcomic Series greater-expanded Gerosha universe, Extirpon's one weakness is - ROBOTS! Why? They have no soul, no spiritual guilt, and their pride can only be simulated by a program. With no free will and therefore no sins, there's nothing to feed Extirpon's power.

Western Animation

 * Megavolt on Darkwing Duck is an electricity based villain shorted out by water.
 * The Liquidator on Darkwing is intimidated by "a common cleaning sponge" and (in a Shout Out to John Kendrick Bangs "The Water Ghost of Harrowby Hall") by being locked in a freezer, as well as by cement and pudding mix(!).
 * Similarly, on a Cartoon Network bumper, Jan of the Wonder Twins says "I could get beaten by a sponge! It wouldn't even have to be an Evil Sponge!"
 * H2Olga from The Fairly Odd Parents has the unique ability to be defeated by Ultra-Absorbent Diapers.
 * In Spongebob SquarePants, the Dirty Bubble, archnemesis of Mermaid Man and Barnacle Boy, has them trapped by his "awesome surface tension." Spongebob SquarePants inadvertently defeats him by accidentally popping him with a pencil while asking for an autograph.
 * Static Shock's protagonist had electromagnetic powers that went on the fritz along with every other gadget in the world when there was a lot of sun spot activity.
 * Static also defeated a water-based villain using an electric current, thus breaking the water down into its components (he even calls the process, electrolysis, by name).
 * However being splashed by water can short out his ability if he's currently charged up.
 * In Disney's Hercules series, a monster steals the powers from heroes and demigods. Hercules then realizes that some of the powers carry crippling weaknesses, such as bright lights interfering with super vision, and uses that to trip up the monster.
 * Stitch of Lilo and Stitch is super dense and while that gives him super strength and endurance, he can't swim.
 * Because benders channel their powers through martial arts, binding or paralyzing their limbs is an effective means of defeating or imprisoning them, though sufficiently skilled benders are able to get beyond this.
 * Both Earth- and Waterbenders have a wide variety of moves to choose from, but require quantities of the element to bend, giving them a disadvantage in ocean and desert environments respectively.
 * Fire- and Airbenders always have their element at hand, but also have their own weaknesses. Fire requires stable breath control to use (making it easier to lose control or tire from using the element), is less effective in cold or at night, and lacks many defensive moves. Likewise, Air Bending has fewer offensive moves, and the culture surrounding it is quite pacifistic, making it especially difficult to finish a fight.
 * Toph's Disability Superpower is rendered completely useless when not in direct contact with Earth . She is extremely apprehensive riding on Appa, gets a view comparable to static when on sand, and is seen having to hold onto her companions when traveling on a wood-built village. It doesn't stop her from intercepting catapult weapons fired from another ship on water though.
 * With Metalbending having become a full-fledged bending discipline by the time of The Legend of Korra, the sequel series also shows the bending style's weaknesses: they are very susceptible to electric attacks due to using reels of metallic cord to attack with. They also have no means of manipulating purified metal due to manipulating earth-based impurities as opposed to the metal itself.
 * In Exo Squad, Neosapiens are stated to have heightened senses. Early on in the show they flashbang one to great effect.