Signs/WMG

The aliens were no smarter than humans.
Everyone always assumes that just because a species is capable of interstellar travel, that means they must have unimaginably superior intellects. But this is a drastic case of You Fail Logic Forever. Human beings have been improving our inventions for eons and throughout all the thousands and thousands of years of constant technological advancements our brains have not evolved in intelligence to a very significant degree. In the amount of time it would probably take us to make it all the way to the point where we can travel to another galaxy—say, another few hundred years—we certainly still won't have reached that point. Probably not even in another few thousand. Especially not now that we're evolving less than before. An alien species analogous to our own in advancement would presumably be the same. That's how evolution works. When you get to a certain point, your brain doesn't need to evolve much more. Evolution is about survival in the wild, not technological convenience. You can't just automatically equate technological prowess with intelligence like it's an automatic given. Think, people. THINK. Don't assume. Think. These creatures are, if anything, less bright than humans—or at least than some of the smarter humans. The way they're hard wired, they seem to be better at long term planning than short term problem solving. They can set up tricks and traps and invasions well enough, but when confronted with something they didn't expect they always seem to miss the frickin' obvious and they don't know how to deal with it. If they were as brilliant as everyone thinks being capable of interstellar travel magically automatically qualifies you as being then they wouldn't act in such a way. This isn't an inconsistency: rather, it is a more or less realistic depiction of how such a species may be on a strange new planet.
 * Technically not entirely true. If they can make stuff, like starships or power armor, that doesn't make them smart, but they also used starships, so they understand (at least) basic principles of mechanics. They seem to understand human psychology when they take hostages. Like monkeys. Stupid - yeah, but not as stupid to be incapable of making power armor suits and using them. Yet they fail...
 * The ones who built the starships, and the ones who fly them, are the ones who understand at least basic principles of mechanics. The ones who were down on earth might actually just be cannon fodder. Or to put it another way, majority of us don't know how to put together an airconditioning unit, much less an airplane or space shuttle. Why should they?
 * Actually any species advanced enough to invent Interstellar travel will have modified their genome to increase intelligence. Its discussed in Stephen Hawking's Universe in a Nutshell. Artificial wombs would have to be used however as the increased brain mass would make normal childbirth impossible.
 * No, just no. Hawkings pet beliefs about about aliens are hardly more credible than anyone else's.
 * Our intelligence has not improved, no. But our knowledge has increased. And we have, in fact, become more intelligent by proxy. We do not become more intelligent, but our machines can, and have.

The aliens we see are mass-produced "grunts", and the important aliens were still in space observing how they handled the strange planet.
Since the grunts could handle neither the atmosphere nor the hostile locals (nor the primitive door technology), the alien leaders decided not to invade, or at worst to retreat and figure out what to do next.

The aliens were refugees!
Their homeworld underwent some catastrophe that nearly wiped them out. What few survivors there were packed themselves into ships and wandered to the nearest inhabited world. They only picked a planet with oceans of poison because they were desperate. They clearly announced their presence and came unarmed and unarmored. The crop circles were universal signs of "Help us, we're starving. Can you spare some food?" Humans, bastards that we are, tried to kill the people who need us! Sure, it looked like they were gassing and abducting humans, but they were just trying to hug us and share their alien cocaine.
 * Or, when we so cruelly ignored their begging for food, they decided we were nonsentient and decided to treat us as food. (They make a mean jerky.)
 * This sounds an awful lot like the plot to Alien Nation.

The Aliens were created on Earth as part of a Terran plot.
An intergalactic invasion is so incredibly expensive that any land, resource, or slaves one would capture would not recoup your losses. The only resource one could garner at a profit, information, is clearly not what the aliens want. Conversely, as portrayed in Watchmen and half a thousand other sources, the best way to unify the Earth is to create an extraterrestrial threat.

The aliens are incredibly unprepared for an invasion. Therefore, they were bred on Earth as part of a Gambit Roulette by some organization to create a one world government or some other lofty goal. There was nothing more to it than genetic engineering, puppetry, bribery, and sophisticated light shows.
 * Yeah, it's the "best" way... just like how the U.S., Russia, China, France, etc. all put aside our differences to battle our common enemies in World War II. And afterward we all stayed friends and held hands and sang Kumbaya. Oh, wait...
 * Yep, we all know Hitler was an extraterrestrial. Someone decided to whip up another one...
 * Well, I think the idea is that the threat should persist indefinitely, thereby keeping everyone constantly united and fighting against it.
 * And all this was orchestrated by the smartest man on Earth.
 * No. It's all just a ploy by the soda companies to sell more soda! Or perhaps more Dasani water.

The aliens are from another dimension, not outer space.
What else could possibly explain their complete lack of preparation or equipment for landing on a mostly toxic planet? They are primitives who stumbled through a portal.
 * Hmm, from another world, seemingly supernatural powers, water harms them... witches from The Wizard of Oz, anyone?
 * What, you mean with the little girl in the sparkly red shoes? And the guy who's scared of everything, and the guy who isn't in touch with his own emotions, and the guy who's smarter than he looks? Nah, couldn't be The Wizard of Oz...
 * Primitives with invisibility-capable spaceships?
 * That isn't an invisible spaceship, it's alien hoodoo magic.

The aliens we see are the remnants of the splicers from Rapture.
The allergy to water is one of many possible results of the long-term genetic damage they did to themselves with the constant splicing, as is their appearance. It also explains how they got on this planet in such large numbers without someone noticing and gives them a proper motive for wanting to capture a bunch of people: ADAM.
 * Problems with this: Rapture itself is a leaky underwater facility, which would've been likely to kill anyone unfortunate enough to have an allergy to water - though admittedly, that would make a strong incentive to leave. And BioShock (series) was released well after the film, which means M. Night Shyamalan must be the precog he tried to tell us he was in Lady in the Water.
 * We will pay for laughing him off. He was our best hope to prevent us from being alien snack food.

The aliens are just plain stupid.
This is why they invade a planet full of poisonous chemicals with no weapons, armor, or reconnaissance. They are incapable of any invasion strategy other than "Hurr, hurr, let's land on that planet and beat them up!'' because they are stupid. They just stole their advanced technology from smarter aliens.
 * It's Beavis and Butthead: The Alien Version. "Uhh huh huh... Let's take dad's spaceship for a joyride to the place they told us never to go!"
 * Or their smarter ancestors made the spaceships a la Idiocracy. This is their version of suburban sprawl. And the next moon mission is gonna prove deadly for the astronauts.
 * My God, Bill Hicks was right all along.
 * This is actually the best hypothesis, as most of the rest could be rephrased as this. Smart aliens would use proper weapons or communications, environmental suits, spectrometers etc., or they would just synthesize anything they want.

The aliens were Criminals
They had been given life sentances, but were told that if they spearheaded the invasion they would be pardoned. The alien government knew they would all be killed.

The "Aliens" were not sentient at all - they were just smart animals.
The real aliens were shipping some fragile space monkeys to the galactic preserve. Unfortunately, due to an error in the delivery form, they were unloaded on the wrong planet.

The aliens weren’t naked.
They were completely covered in biomechanical suits (hence no visible genitalia). The suits were green either from being powered in a way similar to photosynthesis or by having a high copper content (which turns green due to oxidization). The suits, while capable of keeping the creatures safe from breathing in the water vapour in our air, were (unfortunately for the aliens) not able to stand up to liquid water. The one that attacked the Hess home was not killed directly by the water and/or blunt force trauma but, between Merrill’s hits and the water, caused the biomechanical suit to malfunction and tears in it leaked in the vapour rich air which seeped into its lungs causing asphyxiation.

The aliens are The Buggers.
Signs is a prequel to Ender's Game The aliens communicate through bug-like sounds, and they have a hive mind, which explains why they didn't have water protection since they didn't value their lives. Also, their poison neutralizes the harmful effect of water, making the humans harvestable.

The aliens created the DHMO hoax after the movie
only in this case it wasn't exactly a hoax but a way of using our scientific illiteracy against us. hacking into the interenet (our just casually creating their own site) they would gain the support of environmentalist groups which would eventually gain a lot of support and eventually ban the "harmful" chemical and allow them to invade easily, with the added bonus of the human population being wiped out from lack of hydration, the aliens would then colonize the planet.... at least that's how they thought it would turn out, naturally one of the cleverer of the 6 billion monkeys caught on and exposed the "hoax". as for why the aliens thought this would work well, they basically came to a planet made up of 80% liquid death, they're not particularly the brightest star in the galaxy

The aliens were drunk
They were having some wild party (hence naked), but got locked out from their spaceship without keys. The water thing? Alien hangovers are that bad.

The aliens were committing suicide.
Like Suicide by Cop, except it was Suicide By Invading Watery Planet And Getting The Natives To Kill You With It.

The aliens were just showing off. Invasion was not their goal.
Any race capable of interstellar travel in spacecraft that can turn invisible ought to be smart enough to have proper weapons and strategies for invading Earth. Their strategy was woefully inadequate, and their weapons were nonexistent; therefore, invasion wasn't their goal.

Things the aliens may have been doing other than invading:
 * 1) Hunting humans for sport.
 * 2) Undergoing a manhood alienhood trial.
 * 3) Messing with a primitive planet on a dare.

Whatever they were doing, the aliens intentionally handicapped themselves—choosing a planet two-thirds covered in water and limiting themselves to hand-to-hand combat—to show off how tough they were.

The aliens were trying to make a peaceful First Contact.
They were just lousy at it.

Think about it. They went to a planet that was covered in poison with no protective gear and with the worst invasion strategy ever. The kidnappings were retaliation for attacking their ambassadors. ""Open the Gunports, nothing can go wrong!""
 * Or their First Contact manners are similar to the Minbari's.

"Alien: We have experimented with all the beings of Earth, and we have learned that you are the most intelligent and wise. Cow: Why did you turn some of us inside out? Alien: Oh, that was Carl's fault. He's new. Alien (Carl): Yeah, sorry about that, my bad!"
 * Just like the South Park pilot:

The Aliens were after some specialized resource, and actually won.
The aliens weren't here to conquer the earth; they were here for resources. Something in our bodies is valuable to them. It's like miners going into a mine to dig for gems or coal. There's a known risk of methane gas for miners, and a known risk of water in its many forms for the aliens. Chances are some of the miners, and some of the aliens, will die; but the payoff is high enough to make it worth the risk. So yeah, a couple died, (at least one) unfortunate, but they knew the risks when they signed on, and the rest made it out with what they came for.

The aliens lost a ship carrying a VERY important thing at Roswell
They didn't know where the ship was hidden on the planet, so they invaded everywhere at once. Once they got the missing thing (treasure, a resource, whatever) from Area 51, they sent out the signal to go home.

The important aliens are far more powerful, and they destroy the Earth after the movie is over.
The weak aliens were a test to see if we were Xenophobic. If we had made peace with them, they would have brought us into an alliance.

The Aliens were invading Earth FOR the water.
Think about it. If the aliens are vulnerable to water, then they likely did not evolve on a planet with water. Water isn't exactly a common molecule in space. They want the water as a deadly weapon they can use against their kin. The Signs were business proposals to obtain the water peacefully: They wouldn't want to divert resources from fighting their enemies. (That's also why the invasion force is so small.) When that failed—well, humans are mostly water, so they'll separate us into water and human jerky.
 * Why not mine some comets, or an Ice World like Europa?
 * Because of the last WMG - they're idiots.
 * They are mining comets, but comets are a lot smaller than Earth is. They can't mine Europa because there's no way for them to get leverage—there's no place on the surface of that moon that isn't outright water. We can walk on black Hawaiian lava if we're willing to melt our sneakers, but we can't touch the red lava. For someone who can't touch water, the difference between farm fields and ice balls is similar.
 * If they wanted water, even if it absolutely had to be from Earth, why bother getting out of the ship at all? They could just fly in over the middle of the Pacific, lower a pipe, and pump the hold full. Or if it had to be fresh water, they could go in over one of the ice caps and use a crane. There's no need to expose fragile alien flesh to the horrible death world in the first place.
 * Water is actually the second most common molecule in the universe.
 * Not in their corner of it.
 * Water is H 2 O. Hydrogen is actually just a proton and electron. It is everywhere, it is produced by stars and radioactive nuclei. Lots of oxygen was made when population III stars gone nova, which spread across universe - there are no pop. III stars now, so everything is made of them. That means lots of oxygen and even more hydrogen everywhere.

The Aliens are on the run from a much MUCH scarier race.
They just stopped by earth for a bite to eat...they were running out of food, and desperate enough to head towards Earth for food. They sent a few agents ahead to plan the attack, thus, the crop circles. Oh, did I mention the above mentioned "Much scarier race" is heading for Earth, and won't be as easily repelled?
 * Hungry aliens attacking humans, and later a much more effective species that hunts them shows up? Now, if the xenomorphs show up, the predators' and xenomorphs' blood will react and neutralize into water, which is harmful to the Signs aliens, so all we'd need to fight them off is a storm of firework arrows for shrapnel.

The Aliens needed human slave labor.
The radio said that the aliens seemed more interested in abductions than all-out combat. If they found a world with resources they needed but which had large amounts of water present, they'd need either major protective equipment or a slave species to harvest the resources.

The aliens were just idiots screwing around.
Aliens Bob and George were travelling the galaxy, when Bob spied a peculiar planet.

"Bob: "Hey George, let's go down there and run around naked so we can scare the natives who've never encountered life from other planets." George (the more cautious of the two, pauses): "I don't know. That planet is covered in acid." Bob: "Don't be a pussy." George (beginning to be quite annoyed at Bob's remarks, agrees): "Hey, I learned this trick from Steve that drawing circles in their food supplies really freaks them out.""

The invasion was actually the result of an Interstellar Uriah Gambit
What better way to create a suicide mission than to send the underling to a planet covered (about 75%) in what will literally eat then him/her/it alive. The other troops were probably recruited from prisons, asylums and amongst the dregs of their society. How can their equivalent of coroners complain when there are no remain (melting away during the first rain storm)? Those in charge knew; the troops were told they were to procure Di-hydrogen-monoxide by any means necessary. Society was told that they were tragic losses while on an exploration mission to a deadly planet with barbaric inhabitants.

The aliens were damaged by chemicals in the water, not the water itself.
There's plenty of crap in tap water other than good ol' H20.
 * Death by Flouride isn't much better.
 * Death by Chlorine is good, though.
 * Or herbicide! (Our protagonist lives out in the country.)

The Aliens didn't KNOW that water harmed them
Water isn't naturally blue. Why should the aliens think that the blue pieces of Earth are water? They don't have water on their planet, or not much of it, and they clearly didn't send out any unaliened craft to get the composition of Earth before they invaded. It's entirely possible that they never encountered a watery planet in their voyages and didn't realize what water does. Maybe they never even visited another world before (we really overestimated how much dust the surface of the moon had, after all).

That could have been their first encounter with water. Hydrogen may be the most common element in the universe, but oxygen is a good deal rarer. Or maybe they're only hurt by water above a certain concentration; their breathing on Earth is a lucky coincidence they discovered by trial and error.

The Aliens suffer from a negative reaction to certain ions of water.
Water is not a poison to the aliens, they simply suffer from something similar to aquagenic urticaria, a real world disease where people suffer from a horrible skin response to certain ions in water. This still doesn't explain why they came to a world three quarters covered by water, but hey, it's just a movie.

Water in and of itself is not harmful to the Aliens.
Rather, there is something in the water that harms them. The film has some foreshadowing to support this idea, with the main character's daughter refusing to drink the water because "it has amoebas in it". Some kind of bacteria or virus found in unfiltered tap water (remember, the film is set on a farm which probably has a well rather than an urban water supply) can literally eat the aliens alive.

Not all aliens are allergic to water.
We only see the one alien reacting badly to water. Yes, people in the Middle East fought them off - but it never says they used water. Yes, the veterinarian said they chose landing sites away from water - that doesn't make them allergic necessarily, just not fond of water. Perhaps the one alien that invaded the Hess home was some poor schmuck who happened to have a seriously inconvenient allergy - like humans allergic to peanuts, the sun, vitamins, etc.

Water is not lethal to the aliens.
Perhaps it just hurts them: as we see the skin burns off the alien when touched by water. Want to know what actually killed him? Perhaps it was something to do with Merill beating the SHIT out of him.

Firefighters end up on the front lines.
Firefighters vs aliens. Teh awesome cannot be more obvious.
 * After the humans win, they erect a statue to commemorate the victory. The statue depicts a lone firefighter wearing a gas-mask, fire axe in one hand, severed alien head in the other.
 * So, the Pyro is just training? I knew his insane beliefs meant something!

Graham was right: there were no psychic powers, and everything is thanks to God.
He just doesn't notice that God Is Evil.

The Aliens are only hurt by holy water, or at least water handled by a holy person.
This would explain why they die when a priest throws water at them, but they weren't afraid to invade a planet full of water because it wasn't naturally poisonous.
 * This could mean the aliens are demons.
 * However the news did mention the aliens not appearing around large masses of water, so it's not just holy water.

God Is Evil
It's extremely difficult to think otherwise here. If we're to believe the final five minutes of the film, we accept that God killed Graham Hess' wife (traumatizing an Indian veterinarian in the process), gave his son asthma, made his daughter neurotic about her drinking water, and, last but not least, sent aliens to abduct half the population of the Earth...so Graham's brother could take advantage of a weakness already established earlier in the film and, more importantly, so He could save Hess' son from the asthma he gave him in the first place. Which, in the end, convinces Graham to become a priest again.
 * From a Christian theological view point. . From a Maltheist theological viewpoint - yes, God really is that much of a dick.
 * God didn't send the aliens, He just set things up so Graham's family could be saved. (Granted, sans wife, but it is possible that her death had to do with something besides the alien invasion. Possibly him just being a dick.)
 * Remember that it wasn't just Graham's faith that saved him, it was the faith of the Middle Easterners that saved the entire frickin' world. (The primitive method of defeating evil the newscast referred to obviously must have been holy water.)
 * This is basically a heavily softened (his kids live and God doesn't yell at him for complaining) retelling of Job. Whether it counts as evil or not depends on if you grant Omniscient Morality License and nothing else.
 * Nowhere is it etched in stone that the entire invasion takes place solely for Graham's sake. There are generally numerous reasons why things happen. That's part of the whole point of there being no coincidences: everything is interconnected. The world doesn't revolve around one person, you know.
 * Grahm's wife certainly died to save their son from an alien invasion though, which is still a dick move on God's part. As if the brother couldn't figure out to hit an alien with a baseball bat if that hadn't been her dying words.
 * It's easy to think it was all solely for the purpose of restoring Graham's faith, since he's the main character and all, but really, if you think about it, it's very likely the invasion would provoke a similar reaction across the world once the full implications became clear. The creatures eat Humans, which are 60% water, yet water melts them. It makes no scientific sense. And what do you call something that makes no scientific sense but it happens anyway? A miracle.

God Is Good
God did not kill Graham's wife so she could pass on a message. In the scene, when Graham is talking with her wife as she is dying at one point she says to "Tell Graham" which seems a little odd since she is talking to Graham at the time and she did recognize him when he first came up to the car. What if at that moment, she wasn't talking to Graham, but to God? Each "Tell so and so" message was directed at the Big Guy as the last wish of a dying a woman who wanted to protect her family. And, while God doesn't cause evil, He can bring good from evil, and since He doesn't exist in Time per say and can see the whole shebang at once, he granted her dying wish and allowed her to pass on just the right words to Graham to protect him and his family in their coming time of need. It's not so much that God gave the son asthma or the daughter her neurosis about water as He could see from the outside how He could use all these things to help with a little hint or push here or there.

The kids' mother was part alien
Hence Bo's aethereal looks, "premature" smiling, precognition (which we know she inherited from her mom: "Swing away...", etc.), and dislike of water. She's at least half human, so it doesn't harm her; she just feels like it isn't clean.

This also might explain why Morgan is asthmatic and generally sickly throughout the film, but after one shot of alien nasal-spray and a quick nap clears right up (possibly leading to the most energetic reading of "Dad?" in the entire movie).

The entire invasion might be a retrieval operation for hybrids. After all, the radio reports did say they were dragging off people. The spacemen might have mistaken the humans' attempts at saving their loved ones for those of kidnappers grasping at their hostages, and acted accordingly.
 * You Fail Biology Forever.
 * Wait, you expect legitimate biology from an M. Night Shyamalan movie?

Signs and Unbreakable take place in the same universe.
Mr. Glass wanted to find a superhero because he knew the aliens were coming.
 * Too bad the one he found was already part alien, what with the water weakness an' all...

The entire movie was a more realistic take on the same concept as Invader Zim
The alien grunts weren't all that bright, and Earth was obviously the last planet their species should ever want to invade. Hence, the aliens we see in the movie were a group of annoying idiots their superiors wanted to get rid of by sending them on a "Secret Mission" to an acidic Death World.

The Aliens weren't Aliens. They were demons.
I'm actually surprised that this one wasn't said already. It may take a bit of background knowledge of Aliens and Demons, particular Abductions. Bringing a little real world logic into this (bad idea? maybe.) but most (probably all) stories of Alien Abductions are actually the result of Sleep Paralysis. Back when humanity didn't recognize the concept of Aliens, people STILL had Sleep Paralysis, but they thought they were instead being tortured or "abducted" by Demons. There's little practical difference, at least to the "Abductee". Strange Lights in the sky have also historically been the result of Demons or something spiritual, until the modern age, where we began to attribute them to Aliens. Take into account that Water, in particular Holy Water, has been a consistent weakness of Demons throughout theological history, and not being able to enter someones home, while normally connected to Vampires, is also a common theme. Really, it all makes sense if you think of it like this. These "Aliens" have no technology that we see (that i remember), We never see their "Spaceships" aside from a few lights in the sky, which could simply be the means of which they enter our reality. They seem to have no greater goal than to terrorize humanity. Take into account that main character is a lapsed priest, which is also very common in stories featuring Demonic Antagonists, and suddenly it all seems quite obvious. If you're wondering, though "Why did the people in the movie call them aliens" well, what exactly would you call them? the Popular consciousness, in both our reality and the movie, simply favors a more Sci-Fi explanation.