Seasonal variation of structural, physiological and growth indicators and the metabolome of the seagrass Cymodocea nodosa, as well as biogeochemical conditions of underlying sediment were studied in two meadows growing at increasing distance downstream from a fish farm in the Aegean Sea in order to assess seagrass performance under stress. Horizontal rhizome production decreased significantly with proximity to the fish farm (0.67 and 1.57 g DW m−2 d−1 close and far from the fish-farm, respectively). This coincided with observed effects on ecophyiological indicators, such as rhizome nitrogen, leaf carbon and leaf δ13C, which were elevated with proximity to the fish-farm. Seasonality was shown by some indicators being elevated in either in the warm (C of all tissues and leaf δ34S) or the cold period (N of all tissues). Growth promoting metabolites (sucrose, fructose, myo-inositol, heptacosane, tetracosane, stigmasterol, catechin and alpha-tocopherol) were lower close to the zone, whereas metabolites involved with stress-response (alanine, serine, proline, putrescine, ornithine, 3,4-dihydroxybenzoic acid and cinnamic acid) were higher. We found that growth-promoting metabolites were positively correlated with horizontal rhizome production, whereas the metabolites related to stress were negatively correlated. Metabolomic fingerprinting of seagrass provides opportunities for early detection of environmental degradation in marine ecological studies.