Short story about a human scientist that gets caught up in the ebb and flow of an alien environment

A Meeting with Medusa? Arthur C. Clarke. The Wiki for this novella says,

Taking place partly on Earth and partly in the atmosphere of Jupiter, the story tells of Howard Falcon, the captain of a new and experimental giant-sized helium-filled airship. When an accident causes the ship to crash, Falcon is badly injured and takes over a year to fully recover.

Later, Falcon promotes an expedition to explore the atmosphere of Jupiter. After several years and many trials, the expedition is launched, with Falcon at the controls of the Kon-Tiki, a hot-hydrogen balloon-supported craft that descends through the upper atmosphere of Jupiter.

As the craft descends through the various cloud layers, Falcon discovers that the atmosphere supports at least two large forms of life, as well as microscopic and bioluminescent air plankton, producing atmospheric sea-fire. One form is a giant jellyfish-like creature (the Medusa of the title) about a mile across, and the others are manta ray-like creatures about a hundred yards wide that apparently prey on the Medusa.

The Medusa begins to show an interest in the Kon-Tiki, and for his own and the expedition's safety, Falcon ignites his emergency power and escapes back into the upper atmosphere.

After his return, it is revealed to the reader that because of the airship accident much of Falcon's body was replaced by prosthetics, making him a cyborg with increased speed and reactions - allowing him to venture further into deep space than anyone, while leaving him feeling distanced from other humans.

Check out its publication history here.