I read that story at lest 30 years ago, maybe more.
I don't think it was a full-length novel, but it was not a very short story either.
There was an underwater farm that raised animals for food for the general population who lived on the surface. It was definitely not a generally underwater civilisation, just a farm. Maybe not the only farm in all the oceans, but there were many more "surface people" than deep-water farmers.
I am afraid they raised sea mammals, not fish. Dolphins or porpoises or dugongs or manatees, I don't remember. Not whales, though. Still not very politically correct, now.
Anyway, I remember very little. The main point of the story was, since the farm was very deep, they could not use nitrogen. They needed helium. Oxygen was not a problem, they had a lot of energy to extract it from water. But helium is rare. They recycled it as much as possible but there was a steady unavoidable seepage. And the surface people did not want to give them enough helium.
I don't remember much but at the end the deep-sea dwellers managed to get their own helium supplies and won the upper hand on the surface people who wanted to pressure them.
Edit
I think I remember that the surface people had space travel, at least within the solar system.
Definitely no aliens, but maybe human space settlers. On the Moon, on Mars, on asteroids... or just artificial space stations.
It is possible that it was the spacers who eventually came to help the deep-sea people, they had access to a lot of helium up there.
But it may well be a false memory.
Second Edit
As per comments by a) beichst and b) Moriarty
a) There are many similarities with Crisis on Conshelf 10 by Monica Hughes
But I don't remember "Gillers", humans who could breathe in water. Also the main protagonist was a lifelong deep-sea farmer, not someone recently arrived from the Moon.
I remember a dialogue of the main protagonist with a "surfacer", on the topic of quality. He was claiming that while "surface grown" beef came in various qualities, underwater farms were only selling to "surfacers" super-top quality. Now can one compare beef with fish ? Well, it is possible, it this was fish bioengineered to taste like meat. That might well be the cas in my story. But this point does not seem to be explicit in Crisis on Conshelf 10.
If fish in the latter book tastes like meat, and helium is more important than beichst claims, then the plot of Crisis on Conshelf 10 converges to mine. The deep-sea farmers might well have been on the verge of rebellion because of the stinginess of the "surfacers", and help from the Moon on the specific topic of helium might have avoided violence. After all, I might have forgotten the "Gillers".
I know I can have false memories. It is possible that the "GIllers" are a false absence of memories.
But two things I am positive of :
the crucial importance of helium
the "super-top" quality of sea-produced food, so it had at least to taste like meat, but bio-engineered fish is indeed a possibility.
b) I was aware when I first posted of the plot similarity with Asimov's "The Martian Way". I seriously considered mentioning this similarity, but decided against. Maybe I should have.
However, the crucial point in "The Martian Way" is that the Martians dit it all by themselves. In this story, I have a doubt : did the deep-sea dwellers solve their helium problem completely by themselves "à la Martian", or was the alliance with "Spacers" essential in bypassing the stinginess of the "surfacers" ? That would make a significant difference with "The Martian Way".