Life Cycle Analysis (LCA) allows a holistic assessment of the environmental impacts associated with a good or a service, considering its life cycle from the production of its energy and inputs to its disposal. We used LCA to assess the impacts of aquaculture systems and to raise some key questions concerning its development. We compared three production systems of carnivorous fish in Europe: trout in fresh water raceways, turbot in an inland recirculating system and sea bass in sea cages, to explore the environmental impacts of aquaculture. Eutrophication strongly depends on the feed conversion ratio and thus on the efficiency of the system. Energy use is strongly associated with water management options and feed production. Climate change depends on the use of energy resources. It is strongly affected by feed production and feed transformation on the farm. Net primary production use assesses the amount of carbon from photosynthesis used to produce a kilogram of fish. Identifying this impact makes it possible to compare the performance of different farms as well as data on wild fish. Differences between farming systems and among farmed fish species tend to be larger than the differences between fish from aquaculture and fish from fisheries. In particular, the effect of feed composition is discussed. Water dependence, that is to say the amount of water entering the farm per kilo of fish produced, can be used to compare farming systems and assess the links between the farm and its natural environment. LCA results can be used to present a relative environmental profile of farms. The relevance of the different impacts is discussed according to the regional contexts of production which affect availability of energy resources and vulnerability of the environment.