I don't want to be all doom and gloom, and should add that some of these problems are potentially solvable, even if the solutions themselves have trade-offs.
For example, aquaculture can be moved offshore to large farm, mobile farm vessels, so the pollution is spread about instead of being concentrated at a small section of coastline. These vessels are new though, and an accident or freak weather even could result in millions of farmed fish being released to the wild - farmed fish are not the same, genetically, as wild fish, so the effects on wild stocks from that many escapes could be significant.
Another new solution is closed-containment aquaculture, where the fish are placed inside a sealed sphere in the ocean. This approach allows all waste to be collected at the bottom of the vessel, and then turned into fertiliser. There are welfare concerns around increased stocking densities, and shutting hundreds of thousands of fish off from the outside world.
Another solution that is (inexplicably, IMO) seeing huge investment are land-based, RAS (Recirculating aquaculture system) farms. These too can collect all fish waste, and it's touted as a way to prevent disease. There are concerns here too though - using arable land for fish farming doesn't seem like a very good idea, RAS farmers use horribly high stocking densities (they must, to be profitable), and there have been several incidents where disease has been inadvertently introduced from the outside (in such close quarters, the effects are of course disastrous).
OK, so that still all sounds pretty gloomy - realistically the only way for things to get much better is through regulation. But better welfare increases farming costs, and like anything, there is always going to be a race to the bottom (e.g. if Norway increases costs too much for farmers, more move to Chile etc).