In chapter 6 Noah was to take two of every kind, but now in Chapter 7 he is to take seven pairs of every clean animal. This becomes important later when Noah sacrificed to the LORD.
Every living creature? It is clear God meant only mammals and birds, not every living being. The fishes hardly noticed.
It was cold. Ice covered Northern Europe, Northern Asia and Northern North America. The ocean levels was about 400 feet lower than today. The CO2 level was about 180 ppm, less than half of today and could barely sustain plant growth. On the ice it snowed less than half of what snows on Greenland nowadays.
Then something happened. The ice started melting and the ocean levels started to rise. As we used to say in North Sweden, “Spring is not a season, it is a natural catastrophe.” One possible candidate for the flood was in the Persian Gulf, which got inundated about 10000 years ago. While probable, it is a gradual rise, not the catastrophic rise mentioned. A better candidate for the flood is the melting ice cover in the North. The ice melted rapidly and formed ice lakes south of the receding ice, both in Europe-Asia and North America. The water rises year after year, and suddenly it begins to form new rivers going south. When they break through the soil erodes and the lake empties suddenly. So it was with the Caspian sea, that made it rise until it finally emptied into the Black Sea.
And with this rapid ice melt came the deluge of rain. With the rapid ice melt the land under the ice rose rapidly, making the earth more spherical again. In fact, this is continuing to this day with the Bothnian bay rising out of the water by 3 feet per century and the Hudson Bay rising by four feet per century.
(Later the water emptied out in what is now Sweden, having risen out from under the ice.) The springs of the great deep burst forth, this was probably associated with a large number of earthquakes bursting forth geysers and springs in many places.
Yes, it is The LORD that opens and shuts.
Yes, the fishes and whales kept on swimming.
Here is another possible place for the Ark to have landed on Mt Ararat. The dimensions are right.