You hop off and swim while the water-borne pokemon on which you were riding dives down, grabs your bag, and comes back up with it.

Makes you wonder though.. since what keeps your pokémon from getting attacked by the endless Tentacool swarms on it's way down due to that odd nature to attack trained Pokémon.

Indeedy. And with no trainer to guide their moves and tell them how to act, what happens if they faint due to poison? Now you're REALLY screwed.

But what if said pokemon is immune to poison and is capable of defending itself, say a Tentacruel?

I suppose it depends where your cannon is from. After all you can still surf on a fainted pokemon.... But I suppose there is a reason that 1) in the games you can only swim in certain areas. 2) in the anime they always take boats everywhere.

I suppose though, you imagine the storm scenario like what happened with the first movie.

Hell, even if you just happened to drop a pokeball in the grass somewhere. Or in a cave. You dropped your Kadabra that knows Flash in the dark cave and you don't notice until after you've left. Good luck finding it.

Oh, and you happened to drop your HM bag in there, too. Can't even teach it to a new Pokemon.

how do you think you find all those dropped items in the games? although the pokeballs have a teleport system so I'm not too worried about poekballs with pokemon in them. But it isn't supposed to be realistic though so its fine. besides, instead of using flash, you use a flash lite. Instead of using cut, you go around the bush or climb over it.

Oh there's a teleport system?
Wel that fixes at least one of the issues I have. How long does that take to activate, I wonder. Do you need to register the pokeball serial number with the PC? I wonder how open to abuse that is if you saw a friend with a pokemon you wanted that they hadn't registered yet and you just take the serial number and claim it yourself...

Its pretty much instantaneous. I believe it is automatically registered just like with the pokedex. It is rather interesting because remember, the instant you catch a 7th pokemon, the 7th pokemon (in most circumstances) is automatically teleported. But not always. Sometimes you can choose the pokemon from your team to send to your storage box.

I would assume with surf a typical mode of transit that any such sack has a mositure detection sensor or depth gague and a pocket that contains an inflatable capsule to ensure it floats to the surface. Any society that can create transendental spaces and teleportation can figure out a way to ensure you don't lose your bag.

Who keeps their pokeballs in their backpack? Anyone who's anyone keeps them on their belt.

honestly i think we need a good action rpg of pokemon. no turn based battle screens and etc. give us skyrim with pokemon..
i want to see the birth of the pokeball and the time when pokemon masters had to keep hundreds of pokemon on ranches because they couldnt shrink... or digitize.. or whatever happens to them.

It's been shown in the Anime and in the Manga also that pokemon can force themselves out of the pokeballs when they know the situation requires it (Or just for the hell it of, damn you Psyduck/Wobbuffet). They also don't require their trainers to use attacks or know what to do to defend themselves if they are split up. The whole trainer command thing is simply a way to create a greater bond, and to help each other with tactics. Pikachu in the series has been split up from Ash multiple times, and has attacked Team Rocket and the likes in a style that Ash would usually tell him to as one example.

If in your scenario, the pokeballs and the bag began to sink, the sinking pokemon would force themselves out and grab the bag, and swim to the surface. Even fire types (including Charizard) has been shown to swim underwater, leading it to believe that attacks are different to natural water, so if they wouldn't sink like a Golem, most pokemon could retrieve the items.

Talking about not relistic how about Skyrim? I mean living in a land where dragons appear out of thin air, you can use magic, and you can shout somebody into a low "earth" orbit using just your voice isn't overly realistic either.

Now, see, the point is over here and you're aiming all the way over there.

We don't see it in the anime, and is pretty much glossed over in the games, but I can think of one solution to that. The backpack stores your gear in the same way the pokéball stores pokémon. If that's the case, it would probably be possible to access it remotely, probably with a special system. It would be troublesome (needing special equipment), but it could be done, if only to rescue the trapped pokémon.