The principles of organic farming espouse a holistic approach to agriculture that promotes sustainable and harmonious relationships amongst the natural environment, plants, and animals, as well as regard for animals’ physiological and behavioral needs. However, open aquaculture systems—both organic and conventional—present unresolved and significant challenges to the welfare of farmed and wild fish, as well as other wildlife, and to environmental integrity, due to water quality issues, escapes, parasites, predator control, and feed-source sustainability. Without addressing these issues, it is unlikely that open net-pen aquaculture production can be compatible with the principles inherent to organic farming.