Due to its role in the crustacean moulting process, N-acetyl-beta-d-glucosaminidase (NAGase) is interesting to monitor the good proceeding of the moult cycle, as well as relevant in assessing changes in the moulting process caused by stressors. The present study aimed to measure the NAGase activity to monitor the moulting process of the freshwater amphipod Gammarus fossarum. Firstly, an optimised protocol measuring the NAGase activity was made, allowing a robustness and reproducibility of measurements. Then, intrinsic variability of NAGase response was checked under two physiological factors: the gammarid moult cycle and gender. For both genders, a significative increase of activity was observed during premoult, instead of a basal activity detected during postmoult and intermoult. However, the NAGase female profile was preconised to study since it was defined with more precision. Finally, a 16-day exposure of female gammarids to different levels of treated or non-treated wastewater effluents was made. If delays of tissue development appeared on effluent exposed specimens, NAGase activity was similar between the different conditions. This apparent desynchronization between tissue and molecular activities accentuates the diagnostic of moult impairment and raises the interest to use markers at different organisational levels.