Rearing conditions can affect fish morphology, physiology, and welfare in several manners, for instance given the different hydrodynamic conditions or stocking densities. This preliminary study aimed to evaluate non-invasive tools to understand if and how the farming system can influence external shape, skin pigmentation, and freshness evolution during refrigerated storage of European sea bass and gilthead sea bream. A total of 100 individuals (50 sea bass and 50 sea bream) were obtained from a fish farm (located in Piombino, Italy) equipped with floating cages and inland tanks. Fishes were photographed in lateral aspect to analyse shape, while skin colour was analysed with a colorimeter. Freshness and Rigor Index were observed during 7 days of refrigerated storage. Results showed that shape and colour analyses can be useful tools to discriminate fish farmed under different conditions, i.e., marine sea cages and inland tanks. Moreover, farming conditions significantly affected rigor resolution and fish freshness, especially in European sea bass.