Sea ice algae are highly specialized microalgae adapted to grow and thrive in the extreme environment of sea ice brine channels and at the ice-water interface. They usually form the first vernal algal bloom in sea ice-covered waters and represent therefore an important source of high-quality food for grazers before pelagic phytoplankton production starts. Essential long-chained polyunsaturated fatty acids (PUFAs) are amongst the compounds that are considered most valuable for all other organisms in the food web. In addition, various lipid compounds are frequently used as trophic markers for assessing the importance of sea ice algae in food webs. Recent studies indicate that ice algal lipid metabolism is heavily affected by growth conditions and the physiological state of algae, resulting in a strong variability of lipid content, fatty acid composition, but also the composition of highly branched isoprenoids (HBIs) and sterols. We analysed here the spatial and temporal variability of sea ice algal lipids from a coastal site in the Canadian Arctic, and compare our findings with a similar study from Svalbard. The impact of different environmental factors, in particular differences in light intensity and nutrient availability on the lipid profile of sea ice algae is shown. Under limiting nutrient conditions and prolonged exposure to high light, sea ice algae start storage lipid synthesis which is reflected in a decrease in PUFAs. Understanding how environmental conditions control algal lipid synthesis and composition is important for judging their nutritional value and how it may change under future conditions.