How did Noah preserve fresh water fish?

To clarify, a number of literalists that I've spoken to about this subject cite "miracle" as their explanation. This is exactly the point that I'm trying to make in the last paragraph.

IMO, the question here extends far far beyond just fish; for example, you destroy all the plants and all the habitats, and all the insert / etc life that goes with it; you have no food (vegetable or meat) to sustain people or animals disembarking. Remember that a lot of the animals getting off the boat eat other animals, are specialized at that, and would need more than a few to raise young. Any time they eat, they drive another species extinct, and probably doom themselves if they are specialists. So they have the fun job of sitting in the fetid mud surrounded by debris and rotting carcasses, little food, little hope; floods do not sweep things clean; they leave foulness. Let alone the issues of the energy (often from other animals) necessary for the journey back to a climate where it can actually survive for more than a day (which, by foot and paw, could be many months)

My point? (yes, I do actually have one that is relevant): as a result of the issues of the life disembarking from the ark, it seems necessary to adopt one of two positions:

• the rules of life were already suspended to such a large extent (in order to ensure survival of, well, everything that survived) that it is meaningless to ponder about things like how that worked for fish; as a: it isn't recorded, and we would have to invent the reasoning; b: it is immaterial - without supernatural intervention, most of the remaining animal life is going to be dead shortly anyway (also remembering the supernatural intervention required to bring the animals, and the floods); and of course c: genetic diversity is thrown out of the window
• or; it didn't happen as per the tale in the Bible (which to some means: similar divine events, but with Genesis not the exact re-telling, and to others means: any such global/local flood that underpins the story was non-divine in nature)

Each is entitled to their view of what happened; all I'm saying is: if you choose the literal Bible flood account: then it demands multiple additional (beyond that recorded in Genesis) supernatural events, not just the floods and the arrival of the animals. It is inconsistent to try to find a rational/natural explanation for the survival of (say) fish in the midst of supernatural events.

Noah was command to take every animal that walks on the face of the earth - not those that "swim in the deep."

From Genesis 6:19 - 20, via the Amplified Bible.

And of every living thing of all flesh [found on land], you shall bring two of every sort into the ark, to keep them alive with you; they shall be male and female. Of fowls and birds according to their kinds, of beasts according to their kinds, of every creeping thing of the ground according to its kind--two of every sort shall come in with you, that they may be kept alive.

Genesis 6:17 is equally clear that is only flesh that lives on the earth that shall perish:

For behold, I, even I, will bring a flood of waters upon the earth to destroy and make putrid all flesh under the heavens in which are the breath and spirit of life; everything that is on the land shall die.

The Hebrew Interlinear can be found here.

As such, Noah would neither be commanded to protect sea life (since God was wiping clean "the face of the earth" and not "the waters under the earth) nor would he need any special containers for fish. They were protected.[1]

Interestingly, Genesis 6:20 also says that Noah didn't have to search for the animals, rather they came to him.

The point, however, is that marine life is not "all living creatures on the earth," and as such need not fit on the ark.

Okay, as pointed out in a comment however, there is still a question about how fresh-water fish would survive the flood outside of the ark.

A flood that covers the face of the earth is necessarily going to mix salt water and fresh. How would fresh water survive? Two hypothesis come to mind:

1. God miraculously keeps the waters separate. Note that in Genesis he commanded the waters to separate from the land causing the firmanent, so this wouldn't be a stretch.

2. Remember that the flood came both from underground and above. As Genesis 7:11 says:

   on that day all the springs of the great deep burst forth, and the floodgates of the heavens were opened

It could be that the fresh and salt water was kept in some kind of balance.

Am I stretching here? Yes. It was a miracle! But the basic point is still satisfied. Noah needn't have done a thing - God himself attended to the needs of marine life.

It should also be noted that many Christians believe the flood to be a local (and not global) event. Indeed, I have seen documentaries suggest that the flood occurred when the Bosporous opened up and flooded the Black Sea. They point to archeological evidence of civilizations at the bottom of the Black. That said, these people are not the "literalists" asked for in the question, so the point need not be pressed here either.

I realize that what I'm about to put forward is not conclusively proven, but it is possible. It's specifically answering from the perspective of young-earth creationists, which isn't the only view out there. (But it is the one you specified you wanted in your question.)

Noah didn't have to save the fish.

Your question makes two assumptions that seem reasonable, but aren't really axiomatic.

1. That the oceans were salt water at the time of the flood,
2. That the fish at the time were already adapted to either fresh water or salt water.

It is entirely possible that at that early stage in earth's history (assuming a young-earth time-line) that the oceans were fresh water, or nearly fresh water. If this were so, there would have been no dichotomy between fresh and saltwater fish.

The oceans gain their salinity because material from land is constantly eroding into the oceans. Both sea water and fresh water evaporate, but all water eventually ends up in the oceans. the reason the oceans are more salty than fresh water is that the minerals can't travel back upstream, so when the water evaporates, the salinity increases. (more here if you want it)

Even secular scientists are saying that most salt-water fish evolved from fresh water fish. Even the young-earth creationists wouldn't argue that. We see it as a minor variation within the Biblical "kinds" Turning from a freshwater fish to a saltwater fish is a minor change compared to the transformation from a dinosaur (primarily reptile from what we understand) to a bird, for example.

One popular YEC view is that likely, at the time of the flood, most sea life was able to live in both ocean water and fresh water because the salinity of the ocean was much less than. During the flood, large amounts of materials would have been deposited rapidly, and as the flood waters receded, the ocean would have been much more salty shortly after the flood than it was before from that fact alone. Over the remaining years, the oceans have become more salty at a slower rate.

A similar argument can be found here.

And another here, with a story about someone who experimented an was able to get salt and fresh-water fish living together in the same tank. There's no reference on the story, but it's certainly possible to try it yourself if you'd like to experiment.

This article Fish in the Flood has this to add:

As a matter of fact, most of them didn’t survive. Over 95 percent of all fossils are marine creatures. They died and are fossilized by the trillions. Many are buried in great fossil graveyards, tightly packed together, choked with sediments, buried before they had time to decay. Obviously, they didn’t live in the environment in which they died. They were transported by rapidly moving water and then buried in sedimentary deposits.