Short answer: The Bible doesn’t tell us the answer to this question, but there are several possible answers.
Bible reference: Genesis 7:22
“All in whose nostrils was the breath of life, of all that was in the dry land, died.”
Some have suggested that freshwater fish, the ones that lived in lakes and rivers, would have died in the salt water of a worldwide flood. They’ve further suggested that freshwater fish would either have to have been on the Ark, or that freshwater fish would have had to have been re-created afterward. Both suggestions are clear violations of Scriptural revelation.
The Bible records that only air-breathing land animals, birds and creeping things [bugs and reptiles, basically] would have needed to be on the Ark. So no live fish would not have been on board Noah’s Ark, even freshwater fish. In fact, the only fish likely to have been aboard the Ark would have been smoked or salted fish, packed as part of the voyage’s foodstores.
Furthermore, the Bible states that God rested on the 7th day, ceasing the work of Creation, so we have no reason to suppose He re-created anything.
There are two possible answers to how freshwater fish might’ve survived the Flood and neither involve fish being aboard the Ark or it being necessary for God to give them a do-over.
1. There are areas of the world where saltwater and freshwater exist together, but they do not mix. So it’s possible that some creatures could have survived in pockets of either fresh- or saltwater.
2. [And I think this answer is likely more probable] Observable natural selection demonstrates that species become more specialized over time. Taking into account that many of today’s species can adjust to both saltwater and freshwater [for example, those who live in seawater but spawn in freshwater], it’s probable that the ability to tolerate drastic changes in salinity was present in the fish of Noah’s day.
For a more technical exploration of this subject, here’s an excellent article by ICR.org: http://www.icr.org/index.php?module=articles&action=view&ID=351