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. Remember, it was raining in torrents, and we can expect that the rain was fairly fresh water. It would be unlikely for any one area to retain such zones for very long during the tumult of the Flood, but on a worldwide scale, some such segregated zones would have existed at any given time. Furthermore, we don't know the tolerance levels of pre-Flood fish for sediment, salt, and temperature.
Modern fish have a great variety of responses to different environments.
Perhaps before the Flood, fish were even more adaptable. There is also the possibility that great amounts of vegetation were dislodged from the pre-Flood continents and remained intertwined during the Flood as floating mats. Many creationists feel that the decay and abrasion of these mats are responsible for our major coal seams, but underneath these mats, the turbulence of the surface would have been lessened. Perhaps many fish found shelter and nutrition under them, as insects may have, on the mats themselves. Even though there is much we don't know about what went on during the Flood, we can see that there is at least a plausible answer that can be proposed to such questions.