- Most aquaculture is not disconnected from natural waterways (sometime its a caged area in a natural waterway). This means depleting resources and waste dumping which hurts the natural ecology.
- The problems of high density farming: genetic diversity issues, antibiotic use / superbug breeding grounds / diseases
- Fish farms use feed made from by-catch creating some incentive for it.
- It can "look wrong." This may cause people to look for reasons.
On the other hand, aquaculture can be a self sufficient facility in the desert that deals with filters etc or even produces vegetables as a by product. I think relatively few aquaculture businesses actually operate like this, but many could be. The two biggest species (by far if you measure by weight) in aquaculture are tilapia (mild white fish for Americans) & carp (strong oild fish for Chinese). Both of these are easy (high density, grain eating, hardy etc.) freshwater species and would be easy to make eco friendly.
*As a hobby many people do aquaponics. They grow plants hydroponically using bacteria to convert the ammonia from fish waste into plant food. Tilapia are a popular choice. I'm not sure if this particular approach is most commercially viable, but it works as a proof of concept for environmentally sound tilapia growing. It sounds like a lot of fun.
From my understanding (admittedly, limited) both ocean trawling and aquaculture are both unsustainable.
Over-fishing isn't sustainable, but that's what we're doing at the moment. Aquaculture uses 'earth' resources to farm fish, which includes fossil fuel expenditure for feeding and transport (based on current energy networks). It also produces waste products in the form of environmentally deleterious nitrogen-rich effluent which is out-flowed into the wider ecosystem.
An economist might label that a better proposition. Generally less depleting of a finite resource... more 'taming' a resource and using other resources to enable that.
An environmentalist would label both destructive (and while they're at it, the farming of methane emitting grain-fed animals for food is equally destructive compared to just eating the grains instead).
Me personally? I'm going to continue to eat meat. Irrationally (from an economists perspective) I don't think I can enjoy eating ocean caught fish anymore though... it seems like we're really approaching the limits on harvesting that resource more than any other today.
Farm-raised fish seem somewhat on the same scale of "bad for the environment" as eating steak (so I'm 'selfishly' ok with that).
The fact that these fish don't have Omega-3 oils or are described as 'the tofu of fish'? ...makes me think we should probably just eat tofu instead.
See: http://www.nicholas.duke.edu/thegreengrok/farmedfish-pnas092...
Recently, I've seen more of a shift to grains, but that reduces the nutritional value of the fish.