Little is known about plankton dynamics in ice covered lakes. Animals at higher trophic levels such as zooplankton sustain themselves with phytoplankton and terrestrial organic matter. Alterations in ice phenology due to climate change Influence phytoplankton productivity. When phytoplankton as a resource becomes scarce due to low light irradiance in winter, grazing copepods must find other food sources to acquire the necessary fatty acids. Terrestrial organic material is low in long-chain polyunsaturated fatty acids (LCPUFAs) compared to phytoplankton, and these LCPUFAs are paramount to copepod survival. However, changes in copepod fatty acid composition during ice cover and the cause of these changes are poorly understood. To get a better understanding on how copepod fatty acid composition develops during winter and early spring, we sampled copepod fatty acid composition and phytoplankton community composition during ice cover and a month after ice off in the littoral and pelagic zones of six lakes in Uppsala County across a DOC gradient. Here we show that 1) the copepod fatty acid composition changes significantly over time and between the littoral and pelagic zone, 2) composition of LCPUFAs significantly differs between zones, and 3) phytoplankton community composition is significantly different over time and between lakes. However, no phytoplanktonic taxonomic group had a significant effect on total copepod fatty acid composition, except for Chrysophytes and Euglenoides that significantly influenced the LCPUFA concentration in copepods. These results imply that copepods graze on particulate organic matter in addition to phytoplankton to account for low phytoplankton availability during periods of ice cover.