the blue light/ the clear atoms of our human air (lines 25-27)
This marks a big division in this poem. Up above, out of the water, you have the world of people. Down below, you have the world of the sea, which is not human. Both the diver and the wreck are intruders in this under-water-world. The way this point gets made in the poem is that above, in the "human air" you can breathe normally. Below, you have to relearn to breath. You have to adapt to a new and dangerous world.
the sea is another story (line 39)
In part, this line helps to make the same point that the "human air" line did. It points out how different the world of the water is from the world of the air. But at the same time, it reminds us that the sea has its own story, and maybe even its own language. The explorer in this poem has come to learn about this different story, to see if some of its secrets can be uncovered. So, in a sense, this poem is about the story of nature, which swallows up humans and their ships. It's a direct encounter between people and nature.
something more permanent than fish or weed (lines 59-60)
There's a little bit of irony in this line. To the speaker, the human object of the ship seems more permanent. After all, it can't swim off like a fish or be torn away like a weed. We know, however, that the ocean world is the only permanent thing down here. This shipwreck will get eaten up and washed away by the sea. The human world is just passing through by accident. The fish and the weeds are here to stay.