Talk In Circles - Underwater

I think that Underwater just talks about the full ecological state of the oceans -you have not only the large wildlife such as whales (possibly the "no one can take her down") to seals or penguins ("a dark silhouette flashes by") to smaller, seemingly more fragile lifeforms like jellyfish (the "green pockets dropping" - coloured green by the colour of the ocean). I may be crazy but to me the song is about the full life cycle of the ocean, and despite all the cruelties people have done unto her, she still fights back and lives on.

"no one can take her down" must refer to the ocean, as do all the "she" pronouns in the song. Of course you can take great big whales down -- that's how there came to be so much attention on them, because some whale species were nearly hunted to extinction.
I agree, the green/dark silhouettes refer to assorted sea creatures.
"green pockets dropping" sounds to me like a reference to breaking waves. As the top of a wave curls over and falls down, it creates a pocket of air that lasts a very short time before it is consumed in the breaking wave. Due to the sun lighting up the shallow water, it can look green from underneath or inside it.

The "dark silhouette" is always a dolphin for me. It's pretty common to see dolphins around when surfing just about anywhere in Australia. Dolphins like a surf too, you know! There is nothing in the world can match the experience of surfing a wave with 6 or 7 dolphins surfing it with you, just below the surface.