I've only seen bits and pieces of One Piece, but I know that Devil Fruit users (people who have eaten a Devil Fruit) can't swim. I never understood why, though. How does this work? It doesn't seem to give arm or leg disabilities, so what would keep them from being able to swim?
It is said that the Devil Fruits are the fruits of Sea Devil, so even if most of them provide a great power, they're cursed. Quoting One Piece's wiki:
The sea rejects the new Devil Fruit user and they become helpless while submerged in water
Also, Oda said in SBS that Devil Fruit users are vulnerable to all types of water, not just salt/sea water. Basically any type of "standing" water (ocean, lakes, rivers, etc) will affect them, while "moving" water (rain, waves, etc) won't.
Overall, I'm not saying the problem is the sea or something inside the users, what I'm saying is that it's both. And as to why users are affected by Seastone/Sea-Prism Stone/Kairoseki, as stated by Smoker:
It gives off a wavelength that is the same as the sea itself
Basically it's a mini solid piece of the sea so that's why Devil Fruit users are affected by that as well...
In my idea, I think it's because the Devil Fruits are the body of the sea devil. So, if we ate one, we can't swim because we have the power of the seas. It's like, we are stealing their powers so they will make us can't swim. That's why people who ate Devil Fruit can't swim.
It's the same as kairoseki (sea stone). Kairoseki is like sea ice but won't melt, and that's why Devil Fruit users can't swim.
Maybe it's because the Devil Fruits have some sort of origin with the Fishmen. I mean, Fishmen are already ten times stronger than a normal human, so maybe someone in the past thought that such power would be too dangerous if it fell into the hands of Fishmen. That's why those who eat it couldn't swim.
Maybe it started out as a feud in the past of the "ancient weapons"- the objects capable of destroying the world. Look at "Noah", the big ship at Fishman island. Maybe it played a part in the Devil Fruits. Or maybe it's connected to the Adam Wood and Eve Tree something which Franky stated.
This is just a guess though.
To add up to the other answer:
"A person who has devil fruit power experiences a lack of energy when gets into the water!" That means, the user lacks minimum energy to show body movements, otherwise, they could swim. Without body movement, the person starts sinking down.
It's also evident that a person doesn't lose power immediately but constantly. The longer he stays in the water, the more he'll become helpless.
The Devil Fruit side effects section in the wiki is worth reading:
My opinion is that because water as a weakness is commonly seen as a demon/devil weakness, hence the name Devil Fruit. And the user's soul is the polar opposite of the sea, which in turn would create a struggle between the 2. And water ultimately wins seeing as how Devil Fruits are rumored to be a part of the sea, causing its wielder to constantly be drained of their power, or in cases of sea stone, causes their power to drain just enough so that they can't use their power.
This is purely speculation, but it is also a very likely theory all things considered.