Calanus glacialis dominates the zooplankton communities on the Arctic Shelf and plays a key role in Arctic food webs. To overwinter, most juvenile copepods (CV) migrate to deeper waters. Metabolic activity is low at that time but nevertheless the gonads start developing fuelled by internal reserves. The timing of this process is not yet known in C. glacialis from the high Arctic although this information would help to fully understand the physiological characteristics of the overwintering copepods. We therefore sampled the same population in the Billefjorden (Svalbard) from June 2012 to July 2013 and studied the gonad morphology in CV. In summer and early autumn, few cells were visible in the gonads. In late autumn, gonads increased in size in CV remaining at the surface and in CV residing at >100m depth. Gonads of CV were largest in January and at that time moulting to adults started. Lipids fuelled gonad growth, as lipid contents decreased from 41% to 20% of dry mass. Our data suggest that gonad development was independent from ambient conditions but triggered internally.