Why did God not judge the sea creatures when the whole earth was defiled because of the wickedness of man (Genesis 6:5, 17-20). Is it because Noah’s ark was the first ship that was built upon the earth so that the seas were undefiled by the presence of man over it? And also in those days the sea and the land were separated perfectly during the creation of the earth. God had the whole waters under the heaven gathered together in one place and then there was one dry land.
He called the dry land “Earth”, the other part which was “the gathering together of waters He called Seas” (Gen 1:9-10). Does the fall at the garden of Eden and the resultant curse is only upon the dry land ‘the Earth’ and not on the sea and the creatures that live in it (Gen 3:17-19). If this is right, why did the word of God say, “…the whole creation groans and labors with birth pangs together [with man] until now..” (Rom 8:22) which includes the Sea and its creatures?
The Bible does not address the issue of the fish in the sea. It may be as you say, that the sea was not defiled at the time and therefore not subject to the judgment. Also, in Genesis 3:17 God only said, “Cursed is the ground because of you.” If so the sea would have become defiled during the flood with the multitudes of dead bodies caused by the drowning people. This would explain why Romans 8:22 says that the whole creation groans to be delivered from bondage and why John wrote about the sea giving up the dead that are in it in preparation for the Great White Throne judgment (Rev 20:13).