Abstract The effects of ammonia pre-exposure on high energy-phosphates and the intermediary metabolism of the marine teleost Goby ( Pomatoschistus sp.) were studied by in vivo 31P-NMR with simultaneous respirometry. No significant effect of ammonia pre-exposure was observed on oxygen uptake, muscle intracellular pH or high-energy phosphate metabolism. Brief metomidate anaesthesia (10 mg l −1) followed by continuous light anaesthesia (1 mg l −1) was used to prevent excessive swimming. This had no effect on oxygen uptake, muscle intracellular pH or high-energy phosphate metabolism.