The downsides of requested by LordOmar:

Aquaculture takes place mostly in coastal wetlands in brackish water. Wetlands, which include salt marshes, mangrove swamps and mudflats, are more sheltered than coastlines and are excellent for aquaculture. Unfortunately, most wetlands are thought of as desolate, unproductive 'wastelands' and are threatened by development. The expansion of agriculture, industry, and urban areas leads to the removal of natural vegetation and land reclamation. Aquaculture also leads to the removal of natural vegetation in order for ponds to be dug. Once the ponds have been filled with water, excess nutrients and waste product are discharged into the pondwater which then infiltrates groundwater supplies and coastal areas. Eutrophication of the ponds is also possible due to the addition of nutrients.

There is also a possiblity of species mixing leading to a decrease in biodiversity. Please see the node on aquaculture escapees.

If aquaculture is to be successful, without causing damage to the natural environmet, there must be an understanding of how a particular ecosystem works allowing specific aquaculture methods to be developed.