Crustacean discards experience stress during commercial fishing operations, due to increased exercise while in the trawl and aerial exposure during sorting of the catch. Physiological stress and recovery were assessed following trawling of two ecologically important decapod species, regularly discarded in the Clyde Nephrops fishery. Haemolymph samples taken from trawled swimming crabs, Liocarcinus depurator, and squat lobsters, Munida rugosa, had significantly higher concentrations of ammonia (0.308 and 0.519 mmol l super(-1)), D-glucose (0.14 and 0.097 mmol l super(-1)) and L-lactate (6.2 and 0.87 mmol l super(-1)) compared with controls, indicating an impairment of ammonia excretion and a switch to anaerobic metabolism. Concurrently, the haemolymph pH of trawled squat lobsters was low (7.47) compared with controls (7.75); however, the reverse trend was found in L. depurator. Initially elevated lactate (7.98 mmol l super(-1)) and glucose (0.73 mmol l super(-1)) concentrations of trawled and emersed (1 h) L. depurator were restored, 4 h after re-immersion along with pH (7.54). Crabs that had been emersed for 1 h had significantly higher concentrations of glucose (0.2 mmol l super(-1)) and lactate (5.14 mmol l super(-1)), and had more acidic blood (7.64) than L. depurator subject to 1 h of exercise, indicating that anoxia was the main cause of physiological stress. Crabs and squat lobsters lost 7% and 9% of their initial body wet weight following 1 h of emersion, although blood osmolarities did not change significantly. While all animals survived aerial exposure in our experiments, sorting of the catch on commercial boats takes up to 300 min, which could lead to mortality or sub-lethal chronic biochemical changes that could compromise fitness.