The aim of this study was to examine species‐specific differences in pre‐ and post‐stress concentrations of haematological, metabolic and hormonal parameters in two Mediterranean fish species, one with relatively high (European sea bass, Dicentrarchus labrax) and the other with low (meagre, Argyrosomus regius) basal and post‐stress blood cortisol concentrations, in relation to different water temperatures. Fish were reared in net‐pen sea cages and exposed to an identical acute stressor (crowding and chasing with a net for 5 min) in three different periods of the year. Results indicated that inter‐specific differences occurred in most of the examined parameters. In addition, within each species, differences between sampling periods existed in plasma cortisol, glucose, osmolarity, blood pH and muscle glycogen concentration. Glucose, lactate and osmotic pressure showed a constant pattern of change, with maxima at half an hour post stress in both species, while cortisol, and blood and muscle pH, were significantly altered only in E. sea bass. No alterations were observed in liver and muscle glycogen concentrations in E. sea bass, while a significant reduction was evident only in the coldest temperature in meagre. It is concluded that there are important species‐specific differences in the magnitude of hormonal and metabolic response to acute stress and that both basal and post‐stress blood cortisol concentrations are affected by the sampling period.