Aquaculture modifies habitat directly through use of space and indirectly through disturbance to wildlife.

Leasing of public space for aquaculture is often granted for free or with minimal charges, carries few restrictions and requires no accountability to address environmental impacts at the conclusion of a lease.

To avoid conflicts with other user groups, aquaculture operations are often placed in relatively remote areas, resulting in cumulative impacts on wildlife from day-to-day operations that include frequent boat traffic, noise pollution and the continuous presence of people within an otherwise wild area. Scientists in Southern Chile have found that this increased traffic limits the habitat available to dolphins that would otherwise frequent the fjords now clogged with salmon pens.

The high densities of fish in aquaculture operations can also attract birds, marine mammals and other predators. Predators can become entangled in and ultimately die in the nets surrounding the pens. They also prey on farmed fish and damage net pens and other aquaculture infrastructure.

In the U.S., aquaculture operations are allowed to use non-lethal methods to control predators, including acoustic deterrents. These loud noises may cause disorientation, pain or hearing loss in marine species, including marine mammals, sea turtles and fish.

Furthermore, noise pollution may result in other marine mammals changing their behavior by avoiding such areas. While U.S. predator control programs are required to be non-lethal by law, it is difficult to know what happens under the water or to estimate the number of predators killed that are not reported. No such requirements exist for aquaculture operations in most countries.