Unfortunately, a lot of farm-raised fish are fed smaller fish from natural ecosystems, effectively shifting but maintaining the overfishing problem.
If you care about omega-3 (you probably should) without contributing to overfishing (again, imho you probably should), get an algal-oil based supplement. Prices are pretty competitive nowadays.
Not sure why you are being downvoted. Salmon (mentioned in other siblings) is a perfect example of over fishing, and the farmed stuff tends to be of terrible quality and fed absolute garbage/treated terribly.
Salmon is found in high-latitude systems around the globe in both hemispheres. Overfishing is something that occurs to populations, not species. Most of the salmon populations that I am familiar with are not over-fished, but have suffered from spawning habitat loss due to dams and logging. Those are major issues and they continue to negatively affect those populations; you are doing the loggers and dam builders a favor by blaming fishing, which is far easier (and more politically palatable) to regulate.
I hope I've not misunderstood but if you are saying vitamin D deficiency is a 'small health risk' then that needs correction. Never mind the validity or not of the paper in question. Anyone reviewing the peer-reviewed literature on vitamin D for the last decade or so would conclude it's a very bad idea indeed to be deficient. For those who don't get much sun exposure, a blood test is recommended and will put people on the right track.
Fish seem to be a very important component of the most healthful human diets, AFAIK, likely/mostly grounded in various aspects of evolution - some more on the side of actual 'selection pressure', some more on the side of chance and 'doesn't break things in a way that really matters' (i.e., successful enough reproduction / survival until ages required for reproduction).
That said, and in light of the comment from https://news.ycombinator.com/user?id=AlecSchueler, in particular - many of the most essential nutrients / 'micronutrients' that are obtained from eating fish are actually not made by fish themselves. Rather, fish 'concentrate' these substances as they go about their own business of survival. For example, vitamin D3, DHA, EPA, etc. Consequently, there are much more readily available 'vegan' sources of these substances, derived directly from the fundamental source(s) - microalgae and the like.
FYI (to all).
Overfishing IS a serious problem. Our activities, in general, are at a scale, and grounded in processes, these days, that produce significant impacts on the environment. Frankly, in the 'great scheme' of things, it doesn't matter a whit. Humans, and even this planet, are not even a droplet in the ocean of the universe, as far as we / I can even get any sort of a solid handle on that concept, now. But, that doesn't absolve us of any responsibility for trying not to absolutely annihilate OUR home.
It's disgusting to be GIVEN so much (none of us had much hand in almost anything that exists now, even what we've 'built' - we can't create atoms, we don't choose when, where, or to whom we are born, many of the opportunities we are afforded in a 'given life', etc.), and treat it as casually as so many do - to be so entitled as many seem to be.
But then, the universe (/ God / gods / whatever concept you prefer) will always have the final say. It'd just be nice to not F things up for everyone else, IMO.
EDIT: I hope the latter bits, above, don't come off as too moralizing - not my intention ... it's difficult to avoid some frustration with some of what the news inundates us with every day, I find.
More importantly - vitamin D3 is also readily produced in our own bodies with enough of the right kind of sunlight (dependent also on skin tone, age, kidney & liver function [etc.], and, ultimately, 'height of the sun in the sky' - i.e., enough ~290-300nm UV rays penetrating the atmosphere at the angle of inclination / solar zenith angle / whichever concept/quantification you prefer). And, this is actually not much at all. While skin cancer is, itself, a risk - this should, of course, be weighed against the importance of vitamin D3 itself. This comment is already REALLY long, but basically, for latitudes close enough to the 'Tropics', typically only 10 - 20 minutes of sun around noon in summer would be necessary. Winter is trickier. Here are a few links that may be useful for more info (in general, Pubmed - searching for review articles, etc. - is usually a good place to start, IMO - depending on how comfortable you are with reading these types of articles, otherwise, backtracing to those that cite them, especially, the efforts at more 'popular press' descriptions of research now produced by journals like Science etc.):
... The 'Linus Pauling Institute' also seems to have, in my past experience, quite good information on 'micronutrients', in particular (with good citations, etc.), for all of Pauling's actual more tenuous beliefs (himself, in later life) about vitamin C:
The fishy thing is how actual scientists do whole studies using only D1 and then draw conclusions.