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.
the water-eaten log the fouled compass (lines 85-86)
These are both images of the power of nature and the weak, and the temporary nature of human creations. Ships are meant to resist nature, to hold out the water and make it possible to live in the ocean, where nature usually runs the show. But when something goes wrong, nature starts to take over immediately. When the ship is still floating, we use compasses to figure out where we are going and logs (here that means something like a ship's diary) to see where we've been. Once the ship sinks, nature attacks and eventually destroys the human instruments. These ruined things are a way for Rich to talk about the destructive power of nature, even when we try our best to protect ourselves from disasters.