If all terrestrial plants were covered in water, this would have led to drastic changes to the earth's atmosphere (it would be equivalent to destroying all the terrestrial plants all at once), which in turn would have led to changes in the ocean. (Think slightly increasing atmospheric %s of CO2 are a problem for sea life? That would be nothing compared to this.) Further, rapid admixture of water from somewhere else capable of causing a complete, worldwide submersion of land very well would have changed the salinity of the water, resulting in problems for various marine animals and vegetation. Any fresh bodies of water would be submerged and mixed with the oceans, leading to widespread death for animals adapted to fresh water.
If we are to take the narrative in a 'literal' sense, it is highly unlikely fish would have just 'carried on'. More likely, the Biblical narrative of Noah's flood reflects an ancestral memory in Jewish tradition of a large, localized flood, or perhaps a global flood that was highly disruptive to human civilization but didn't actually submerge all of the land.
Addendum: if you want an answer sympathetic to Biblical 'literalism', this site attempts to answer the question from that perspective. I believe it understates the problems aquatic life would face from this sort of event, but they conclude that
"Many aquatic creatures were killed in the Flood because of the turbidity of the water and changes in salinities and temperatures. Indeed, the geologic record testifies to the massive destruction of marine life, with shallow-water marine invertebrates alone accounting for an estimated 95 percent by number of the fossil record."