The energetic status of freshwater fish provides a dynamic measure of their energy balance in response to the environment they occupy. Commercially available microwave technology (the ‘energy meter’) provides a rapid, non-lethal and inexpensive alternative to traditional laboratory methods for the determination of energy density. The energy meter requires species-specific confirmation of the water–lipid relationship, and comparison of energy meter readings with laboratory-determined estimates of the whole-body energy density. I explored the applicability of the energy meter to the threatened Murray cod (Maccullochella peelii peelii), using both hatchery and wild individuals. Although hatchery and wild fish varied in lipid content, water content and energy density, the parameter comparisons necessary to calibrate the energy meter were statistically consistent between both groups. Subsequently, a robust combined water–lipid relationship was identified for Murray cod, where energy density was strongly related to both water content and lipid content. Average energy meter readings were capable of providing a rapid, non-lethal and accurate assessment of Murray cod energy density. The successful calibration highlights the applicability of the energy meter to provide a dynamic measure of the energetic status of threatened freshwater fish throughout the world.