High latitude marine ecosystems are characterized by strong seasonality in incoming light and thus primary production and food availability. Polar zooplankton organisms have developed the ability of storing large amounts of lipid reserves to face this variable environment. Lipids are composed of fatty acids, which are transferred from unicellular algae via zooplankton to higher trophic levels. In our experiments, a 13C labeled diatom-flagellate mix was fed to key zooplankton species (copepods and thecosome pteropods) over some days to a couple of weeks to follow the fatty acid carbon assimilation and possible de novo synthesis of fatty acids and alcohols. Fatty acid and fatty alcohol compositions were determined by gas chromatography. The 13C incorporation was monitored using compound specific isotope ratio mass spectrometry. Among the small sized copepods Pseudocalanus minutus and Oithona similis, maximum lipid turnover occurred in P. minutus, which exchanged 2.6% day-1 of total lipid, whereas 0.5% day-1 were exchanged in O. similis. In P. minutus, the diatom markers 16:1(n-7), 16:2(n-4), and 16:3(n-4) were almost completely renewed from the diet within 21 days, while 15% of the flagellate markers 18:2(n-6), 18:3(n-3) and 18:4 (n-3) were exchanged. In O. similis, 15% of both flagellate and diatom markers were renewed within 21 days. Thecosome pteropods, in contrast, are less lipid-rich and less studied, although they can contribute with more than 20% to the zooplankton biomass in Arctic waters. The daily turnover rate of lipid was between 0.15% day-1 in L. helicina and 1.3% day-1 in L. retroversa. High carbon assimilation was found in both diatom and flagellate markers in L. helicina accounting for 0.8% over 6 days. In L. retroversa, 0.8% of the diatom markers were exchanged after 6 days while 13.9% were renewed in flagellate markers. Our methods allow us to estimate lipid and fatty acid turnover rates of specific Arctic key organisms to better understand the carbon und energy flux through the high latitude marine ecosystems.