Well, there are examples of various kinds of fish swimming up waterfalls and such in order to return to their old spawning grounds. Salmon, Koi, or Oman Garra, and such.
...Swimming all the way up from the core of the planet would be a VERY extreme example of that. But, since this is the One Piece World, it's not impossible. There might not be many fish who could make such a journey. But, there are probably a few that could.
So, since these are Shonen battle manga fish, they probably could make it up those "waterfalls" around the holes in the ocean. They're really tough fish! Believe in them!
The thing is, there's some evidence in the series that this entire PLANET is actually "artificial" on some level.
Between the Whales finding the Red Line "unnatural", and the existence of Continent Pullers like Oars that can literally move entire islands around, and Awakened Devil Fruits that have the ability to permanenlyt change the environment around them like on Punk Hazard...I think it's pretty likely that this entire planet has been altered from whatever it originally looked like. Whether it turns out to be Earth in the far future, or someplace else.
If you think about it that way, the All Blue isn't a miracle because it's a natural phenomenon. It's a miracle because something good has come from all the destruction Uranos caused. Even if the All Blue is the result of some terrible disaster or a bloody war...life still finds a way. It's a "flower blooming on the battlefield" kind of situation. Beauty can still be found, even amongst the ruins, given enough time. In some ways, the All Blue even represents some of the core ideals of this series. Everyone, from all over the world, mixing together, so they can become "friends", without any borders standing in their way. It's not just a ideal for fish, but so that all the races of the World can come together, instead of being separated on their home islands. The All Blue doesn't need to be natural to be a miracle, in my opinion.
It kind of depends on how artificial or altered this planet ends up being, by the end of the story, though. There's differing levels of how altered the World could be. But, since there were 3 "Worlds" in the Harley Text mentioned, I'm guessing that this World has been changed 3 times. To fit the desires of 3 different "Gods", probably. So, we're probably in the third version of this planet. And probably soon to be on our fourth.
I have a feeling that this entire World is going to end up being pretty heavily altered again, if Luffy changes it to be "His World". Maybe it'll just be putting things back where they should be in the first place. But, things will likely change pretty dramatically all over the World. At the very least, Luffy's probably going to do something about the flooding, since that's a existential threat to the people of the World. Chances are, we might be looking at a very different planet, by the end of the series.
As far as the practical effects on the ecosystem of the planet...well, I just don't know if Oda is really thinking too hard about that. This World kind of works on it's own logic, sometimes. Things will probably work out, by the end of the story. I feel like Oda will prioritize the metaphor and meaning behind what happens, rather than sticking to pure scientific accuracy. The ecosystem won't collapse, because the new "God" doesn't want it to. It'll probably be that simple. Or maybe that complex, depending on how abstract Oda ends up getting with by the end of the story. Oda IS a fan of Ghibli films, after all. Things could get...weird, by the end of the story.
Although, if you want a idea that leans into something more "naturally occurring", there are options.
For example, what if the All Blue is the only body of water left on this planet that hasn't been altered by any of the "Gods"? The only body of water that's left of what this planet originally looked like, before it started being altered over and over again. The "Primordial Sea" that acts as the origin for all other bodies of water on this planet.
That would mean, it's not so much that the All Blue is created by mixing ocean water from all over the World together. It's that mixing water together from all over the World creates something that's close to what ALL the oceans of this World originally were. The separation of the seas is what's unnatural. The All Blue is what all the oceans should be. But, every other body of water got altered by everyone who was "playing god".
I mean, if all the fish of this World really can survive in ANY of the seas, regardless of the local environment, that kind of implies that all the Seas originally used to be very similar to each other.
OR...maybe the All Blue is literally being created and maintained by a dragon, or some other sea creature?
https://onepiece.fandom.com/wiki/Sea_Currents
Back in Chapter 604, we saw a illustration explaining how the Deep Currents work. Franky described them as "somehow always being connected". And the illustration was of a dragon wrapping itself around the World. Maybe that wasn't a visual metaphor? Maybe that was literally what was going on.
Maybe there's been some Ancient animal that's been making sure the undersea life can still get to different places all around the world by creating these currents by "drilling" the currents under the sea. So that the fish can still reach their original spawning grounds, no matter which sea they ended up stranded in. Or so that it can perform tasks all around the World, as necessary. Kind of like how the Sea Kings are all working towards the same goal, after all these hundreds of years.
This would still be somewhat artificial, but it would be a example of "nature taking care of itself" in a way. The All Blue is created by the migration patterns of a large, powerful creature, deep undersea. Beneath the Deep Currents most of the World knows about, maybe there are the "Deepest Currents" where the All Blue is created. Kind of mirroring how Imu's contract names work. They might mirror the types of currents. There's the Surface Currents, the Deep Currents, and the "Deepest Currents" (in theory). Mirroring Imu's Shallows, Depths, and Abyssal Covenants.
Just a thought.
Personally, I do still think the holes in the ocean will likely play a big part in what and where the All Blue is. But, Oda could easily go in another direction. The story isn't written yet. There's options still on the table. It all depends on where the story ends up going. Time will tell.
