Any activity that uses natural resources or interacts with the environment will potentially have issues relating to it. Aquaculture is no exception. Here are a few concerns about the practice:

Nutrient Pollution

Especially with intensive aquaculture farms, there is an issue of irresponsible waste discharge (including uneaten food, body wastes, and dead fish) from the farms. This discharge results in the contamination of nearby water and soil. If chemicals, nutrients, and foods dissolve in warm water, they cause eutrophication when such waters come into contact with surrounding waters. This phenomenon is known as nutrient pollution. The organic residue that settles on the seabed may also cause an alteration of seabed fauna and flora communities.

Here is an illustration of a basic open-net pen.

Notice how nutrients are added and how fish waste collects at the bottom.

Escapees

Wild stock may face food and mating competition or predators if farmed species get into the wild, either by intentional release or accidental escape. They can spread diseases and just like the concerns of GMO seeds, they may mix up with wild species and soon we will not be able to differentiate between wild stock and farmed species. They may also interbreed with wild stock and endanger some native species, threatening the entire ecosystem.

Habitat Destruction

One good example of habitat destruction is the creation of ponds for culturing marine shrimps. Thousands of hectares of mangroves and coastlands, which serve as nursery grounds for many aquatic organisms have been destroyed in places such as Thailand, Vietnam, and the Philippines. Mangroves also support many marine and terrestrial species and also protect coastlines from storms.

Chemicals Used to Control Diseases

To control bacteria, fungal, viral, and other pathogenic matter, drugs and chemicals may be used on fish farms (ponds and cages). There is always a chance that these dissolved chemicals may come into contact with other aquatic organisms nearby. Too much use of such drugs can also affect humans who eat the fish.