Measuring fish condition should link ecosystem drivers with population dynamics, if the underlying physiological basis for variations in condition indices are understood. We evaluated traditional (K, Kn, hepatosomatic index, gonadosomatic index, energy density, and percent dry weight of muscle (%DWM) and liver (%DWL)) and newer (bioelectrical impedance analysis (BIA) and scaled mass index (SMI)) condition indices to track seasonal cycles in three flatfishes — winter founder (Pseudopleuronectes americanus; three stocks), yellowtail flounder (Limanda ferruginea; three stocks), and summer flounder (Paralichthys dentatus; one stock) — with contrasting life histories in habitat, feeding, and reproduction. The %DWM and %DWL were good proxies for energy density (r2 > 0.96) and more strongly related to K, Kn, and SMI than to BIA metrics. Principal component analysis indicated many metrics performed similarly across species; some were confounded by size, sex, and maturity along PC1, while others effectively characterized condition along PC2. Stock differences were along PC1 in winter flounder, reflecting different sizes across stocks, whereas in yellowtail flounder differences occurred along PC2 related to condition. These comparisons, within and across species, highlight the broad applicability of some metrics and limitations in others.