Carcinus maenas and Necora puber were exposed to air for 72 h and 18 h, respectively, at 18 °C. Changes in the free amino acid (FAA) content of their muscle, hepatopancreas and haemolymph were recorded during air-exposure and subsequent reimmersion. Muscle and hepatopancreas urate contents and haemolymph serum protein levels were also measured during emersion. In air-exposed C. maenas, the muscle FAA pool increased significantly within the first 24 h of emersion. This increase was due to an increase in the non-essential amino acid (NEAA) pool only; the essential amino acid (EAA) pool did not change. In haemolymph, the EAA pool decreased during the first 24 h of emersion, whereas the FAA and NEAA pools did not change. However, in this compartment, glutamine levels increased throughout the air-exposure period. No significant changes in FAA, NEAA and EAA contents of the hepatopancreas were observed during the 72 h emersion. In air-exposed N. puber, the FAA pools of muscle and hepatopancreas did not change, although changes in the levels of some amino acids were observed during the 18 h emersion period. In this species, large increases in both the NEAA and EAA pools in the haemolymph were recorded. High levels of urate were observed in the muscle and hepatopancreas of immersed N. puber, but no significant changes occurred during emersion. In contrast, immersed C. maenas exhibited low levels of urate in both compartments, and hepatopancreas urate levels increased slightly during emersion. Haemolymph protein content did not change in air-exposed N. puber, whereas it increased in the haemolymph of 72 h emersed C. maenas. The origin of newly formed NEAAs and their role in ammonia detoxification, particularly in C. maenas, which is able to regulate its internal ammonia levels during such a prolonged emersion, are discussed.