The nutritional value and developmental variations of cultured fish were assessed for European seabass and gilthead seabream specimens reared in semi-intensive aquaculture systems in two Portuguese estuaries. Quantification of total protein and of carbohydrate and fatty acid profiles was carried out to determine differences between the composition of the same species in two development stages reared in four distinct farms. A significant influence of the rearing site on the nutritional composition of the same species was found for adult European seabass regarding saturated, monounsaturated and highly unsaturated fatty acids contents, both between estuaries and within each estuary. In gilthead seabream, saturated, monounsaturated, polyunsaturated and highly unsaturated fatty acids content were also influenced by the rearing site. Carbohydrate analysis showed a significant influence of the rearing site on free sugar and polysaccharide content in fish of both species, and there was no influence on the species' protein content. Differences in fatty acid and carbohydrate content among juvenile and adult stages were found for all the groups studied. The present study supported the existing evidence that semi-intensive rearing systems are subjected to the variability of extrinsic factors in the rearing sites, influencing the nutritional value of the same species, namely regarding lipid and carbohydrate profiles, depending on the production site. From a consumer's perspective, such differences may come as a disadvantage of the rearing method, as it is expected for a product to provide equal nutritional properties and benefits regardless its origin, especially within the same country.