Create a 1 block deep water filled area, surrounded by 2 block high walls, so chickens must swim. Throw chicken eggs agoinst wall and hatch a few chicks. They will swim for a short time, but will then drown. In earlier versions they would swim forever.
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Confirmed, but I don't know if this is intended.

I guess that is so that some automatic chicken farms are nerfed.

Confirmed - if this is intended it really sucks, in the real world chickens can reproduce without human intervention so WHY should the Minecraft masters want to ruin chicken farms

In the real world, chickens wouldn't be able to swim forever, whether baby or adult 😛

Whether in the ocean or a one-block-deep pool, baby chickens die within a minute. Baby pigs and cows sink and die almost immediately in the ocean. Baby villagers survive to adulthood while bobbing in the ocean – animals should dos the same. [Notes from MC 9492]
I suggest checking to see if this is an unintended consequence of shrinking the hit boxes of the babies. Perhaps they share code for swimming and don't float high enough to breathe.

It's not that they don't swim, it's that they are totally 100% unaffected by flowing water, and I consider that as a bug.

The part that drive me nuts the most is the baby chickens are drawn to the water to play, and aren't start enough to stop before they drown. As soon as I hatch one, it wonders over to the water and dies. (arg)

Three bugs force the design of chicken and other animal farms in this version to be very different from those of the past: Animals living in and "leaking" through transparent blocks, dying because of solid blocks and babies dying in water. I am amazed that it seems these bugs are not assigned nor being addressed before the next release. These bugs are illogical and seriously detrimental to gameplay and they will break many currently working farms and complicate any new redstone designs that are attempted. Mojang--are you listening?

I deleted my comical rant on the mysterious workings of how Mojang fixes their bugs. (it made me feel better just writing it out) but please seriously, please fix this issue ASAP. RJ is correct on how it sucks some energy out of game play. (Mojang) Please let us know what we can do to help you. Thanks...

Yeah, like they said ^^^
You spend all time making this cool grinder, only to find it that it'll suck due to these animal bugs, including the fact that baby chickens don't swim.....

Having this issue with 13w07a as well, doesn't matter if the water is flowing or a static source block. Hatching a chicken into water causes it to drown.

Still exists in the Prerelease!! Noooo! No Auto Chicken farms with water in 1.5 😞 Please update description

@Alexander I found another way to make one, one that doesn't involve water at all 😛
Just make a whole floor of hoppers, then make upward dispensers at the end, with top-half slabs on em to make space for the baby-chicken spawns from the eggs.
Then just attach a redstone clock to all four dispensers. The hoppers will lead all eggs to the dispensers, and they will keep spewing them out as long as the chickens lay eggs, occasionally spawning a chicken 😃
But ye, I can confirm that the problem still exists.

I was looking into this and was able to fix this bug. The problem is that Minecraft adjusts the bounding box for mobs when they are being checked if they are in water (shrinks the height). Because the babies' hitboxes are short, they are shrunk too much and fail.
Can't post the change made to the sources as it is against the ToS unless an exception can be made. However, I will describe the issue without using any code.
@Mojang: Babies have 0.5*parent height and chickens have height 0.7. MC checks for water collision using the mob's height - 0.4. Since the adjusted baby chicken height is -0.05, this will always fail when they are on the ground. Reducing 0.4 to 0.3 allows the chickens to swim.
Hopefully someone at Mojang will be able to fix this before the next update. 🙂
<edit> This bug is caused by MC-1524's solution.

Ok, who do I have to payoff to get this issued assigned to someone so it can get fixed?
<new>
I used the "Hopper fix" and it didn't work as you described. I made a 3x3 room with hoppers for the floor. I added adult chickens and thru eggs in but I could only ever have 4 adult chickens alive for an extended time. Something caused any extra to die, I found a feather and meat in the hopper but not what I would expect for the number of babies that should have grown into adults.

Well, they've said a few times that issues are addressed roughly by vote count, with issues with more votes getting higher priority. It looks like this issue is sitting around 70th place, sorting by votes.

Come guys lets make 20 accounts each and vote this up 😃

With hoppers you should be able to make an even more "automatic" egg/chicken farm than before, and without having to use the ridiculous floating method. I say there's far more important bugs for them to look at.

I like being able to make an egg farm with both redstone or water. Making it with just water makes it less likely too cause lag or bug out. Then later on you can upgrade it once you get more resources, so that it kills, cooks and sorts all the resources.

Figuring out what causes an issue is the hardest part of debugging a program, since AHelper has figured out that the cause and have given them the solution to implement, the only delay is on Mojang side.
My chicken coop wasn't a "chicken/egg farm", it was fenced in 7x7 plot of land with a 1x3 pond centered along the back fence. I feed the chickens, they make babies and the baby chickens go play in the pond until they drown. Sure, I filled in the pond, but what would the chickens drink? I'll have ASPCA on my back because it's in a desert biome...

The reason why chickens die when they grow up is that when they grow up, their hitbox returns to the unadjusted size, causing them to suddenly be inside a solid block. Because they are being pushed, they are shot into the block and suffocate. Placing transparent blocks should help.

Confirmed with baby cows.

still in 13w17a

Still in 13w18c

Confirmed in 13w21a and 13w21b

I don't think this should be a bug. A newborn animal isn't going to be able to swim very well. And this adds a mechanic that people can use in different ways. Like sorting babies and adults.

Do remember that babies swim so long that their BBox hits the water, which was defined expected behavior, and that this new behavior was added from a fix to a bug. For "sorting babies and adults", this bug is the byproduct of that.
Affects 13w23a. Confirmed the effect on baby ocelots and wolves as well.

If this isn't going to be a bug because it's unrealistic for baby animals to be able to swim, then "Minecraft" as a whole, needs to go under a huge change, dirt shouldn't float and should need support underneath, to begin with...

Draven, your logic is flawed. first there isn't a "newborn" stage there's only "baby" and "adult". Secondly baby ducks (ducklings) love to swim, baby horses(foals) can swim across rivers, a baby cow(calf) can swim across lakes, baby pigs(piglets) love to swim, etc. Lastly, you can't use the excuse "well, it's not very realistic for yada yada yada" regarding anything in this game, When was the last time you've seen anyone punch a tree until it fell down? AND CHUCK NORRIS DOESN'T COUNT! (and Melih has a great example also)

Same issue on OSx.

Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.

Tested in 1.6.2 with chickens. If I throw eggs into a 1-block-deep pool of water, they hatch and swim normally. On the other hand, if there are any areas without water (e.g. due to signs or the end of a water stream), the baby chickens will happily land on those dry blocks, then walk into the water like it isn't there (actually, gliding around strangely quickly) and eventually drown. This is consistent with what I observed in previous versions, but perhaps not exactly matching the description of this bug.

Tested in 1.6.2 OS X. baby chickens die in ocean or flat water. Bug still exists.

Confirmed.

I found that if you spawn the chicks over flowing water, they will swim when they fall into it. However, if you remove the water or spawn them on dry land and then add flowing water, it will run over them without them swimming upward, causing them to drown.

Confirmed in 13w39b. On Mushroom island, breeding mooshrooms, two baby mooshrooms walked into the water, sank, and drowned.

This may explain why I keep finding rotten flesh in a pond (baby zombies)

Confirmed in 1.7.2 baby chickens still drowning.

I wouldn't want this fixed! It makes a useful baby mob separator!

Please note that the fix for this does not remove resizing of the babies but instead fixes collision checking for the water. You will still be able to detect babies, but this bug is a side-effect of resized mobs, same with babies growing up inside of blocks and dieing.

Still affects 14w08a.

14w26c, baby chickens float, but others (cows, pigs, villagers) do not.

Poor doggy Greg...

That is 14w30b when baby doggy Greg drowned because of the bug!!!!

Even Iron Golems can't swim! That's obvious since iron is denser than water. They don't drown though. But they would be killed by bunch of creepers, skeletons and zombies if they go on land, so going under water is a better idea than going on land.

Is that a baby wolf not swimming? If so, my fix above is still valid.
Question to all, since the hit box is too low to collide with the water, if you place fences (hit box extends into the above block) on the bottom of water, can someone confirm babies swim? This might work as a temp fix for some cases.

I've just seen a baby chicken float above the water. It bobbed up and down as normal, but barely touched the water itself. If this is because of the sticky motion I described in MC-70700, I can imagine a baby chicken could get stuck below the water's surface and drown.

I think it is fixed in 1.8, but in my opinion it shouldn't of.. babies cant swim in real life.

Confirmed proper behavior for all baby mobs; All babies correctly swim when standing on a block under water, unlike previous versions.

Please reopen this!!! This is reappearing in 1.13. Though baby animals seems to float on water (They will try to get to the surface), they are just perfectly submerged a little bit below the surface and it is enough to drown them)
Edit: Just found out and created a similar but not identical issue in 1.13: MC-134755 I confused that with this issue.
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[media]Adult mobs are not affected. It affects all baby mobs at all water depths