This is a short story, it may have appeared in one of the "Year's Best SF" from David G. Hartwell or "The Year's Best Science Fiction" from Gardner Dozois collection, as I used to read those often.
The title is fairly comprehensive in describing what I remember about the story, here it is again for your convenience: a story about fish with "metal" bones on a water planet where people live in floating habitats with hydrogen tanks below them.
I wonder if this story is Good Mountain like your other question.
It isn't a wholly water world, but there are floating cities, the New Isles, and they do recover metal from fish bones. The sea is rich in iron and the sea creatures concentrate iron in their flesh and bones:
World’s Edge: In some past eon, the city stood on the Continent’s shoreline, nothing beyond but darkening skies and bottomless water. For generations, this great port had served as a home for fishermen, and more importantly, for the brave souls who journeyed onto the trackless sea-hunting giant rust-fins and the copper eels and vicious many-mouths. Fortunes were made from every carcass brought home—great masses of inedible meat and iron-rich bone pushed into furnaces and burned away, leaving nothing behind but a few dozen kilos of precious metal.
The isles don't have hydrogen tanks below them, but they do have methane tanks:
With the best alloys in the world, insulated tanks were built, and they were filled with methane and dangled far beneath each Isle, using the sea’s own pressure and cold to help keep the gas liquefied.
