We studied the seasonal lipid dynamics of Calanus finmarchicus from Loch Etive, a semi-enclosed fjordic environment on the west coast of Scotland, in relation to the diapause behavior of this species. Levels of total lipid and triacylglycerol in individual copepodid stage V (CVs) exhibited clear seasonal trends, with highest levels in June and progressively decreasing through late summer to winter. Wax esters in CVs were more variable, but followed a similar pattern. An index of the level of unsaturation of wax esters, effectively an indicator of the levels of polyunsaturated fatty acids in the wax ester reserves, were highest in midsummer and declined progressively through autumn and winter. Fatty acid analysis of total lipid in the CVs confirmed that the amounts of polyunsaturated fatty acids in the wax esters decreased, while amounts of saturated and monounsaturated fatty acids remained comparatively stable. Polyunsaturated wax esters are selectively catabolized by C. finmarchicus during diapause. Previous studies have linked unsaturation of wax esters in calanoid copepods to the initiation of diapause and buoyancy control, and we hypothesize that selective catabolism of polyunsaturated wax esters is linked to the processes of diapause termination and ascent to surface waters.