To add to liha's nice write-up detailing some of the downsides to aquaculture, the following information should also be considered.

In many circumstances, the species being farmed are saltwater species, meaning that estuary or wetland production, as suggested above, is not a possibility. Under those circumstances, coastal areas are penned-off, and production occurs therein. There are two major problems with this approach. First, these coastal areas are among the most important nursery areas for many marine fish species, and massive aquaculture installations can inadvertintly devastate wild fish populations as a result. Second, the water in these nearshore areas is often considerably warmer than that found in the species native habitat. While this increases growth rates, which is helpful for the producers, it also stresses the animals physiologically and increases susceptibility to disease and parisitism. Further, one thing rarely mentioned when discussing the relative merits of aquaculture is the production of food for the farmed animals. Aquaculture is often mentioned as a wonderful solution to the depletion of the ocean, and as an economically viable manner to produce the fish and shellfish desired by humans without hurting native stocks. However, the production of fish pellets is, in and of itself, highly damaging to the environment. Huge seines, with very fine mesh, are used in the ocean to collect both invertebrates and fish larvae which are later dried and turned into pellets. This has two negative effects on native species. First, many of their young are destroyed in this manner, putting pressure on often already vulnerable stocks. Second, the invertebrates gathered in this way are the principal food source for many of the wild fish species. Taking this biomass (read: energy) out of the food web in large quantities results in lower biomass of the wild fish species that are supposed to be conserved by aquaculture.

Many scientists who work in the field (fisheries science, oceanography, limnology) now believe that in many if not most circumstances, aquaculture can in fact have a greater environmental impact than directly fishing wild stocks.