The Arctic represents an extreme habitat for phototrophic algae due to long periods of darkness caused by the polar night (~4 months darkness). Benthic diatoms, which dominate microphytobenthic communities in shallow water regions, can survive this dark period, but the underlying physiological and biochemical mechanisms are not well understood. One of the potential mechanisms for long-term dark survival is the utilisation of stored energy products in combination with a reduced basic metabolism. In recent years, water temperatures in the Arctic increased due to an ongoing global warming. Higher temperatures could enhance the cellular energy requirements for the maintenance metabolism during darkness and, therefore, accelerate the consumption of lipid reserves. In this study, we investigated the macromolecular ratios and the lipid content and composition of Navicula cf. perminuta Grunow, an Arctic benthic diatom isolated from the microphytobenthos of Adventfjorden (Svalbard, Norway), over a dark period of 8 weeks at two different temperatures (0 and 7 °C). The results demonstrate that N. perminuta uses the stored lipid compound triacylglycerol (TAG) during prolonged dark periods, but also the pool of free fatty acids (FFA). Under the enhanced temperature of 7 °C, the lipid resources were used significantly faster than at 0 °C, which could consequently lead to a depletion of this energy reserves before the end of the polar night. On the other hand, the membrane building phospho- and glycolipids remained unchanged during the 8 weeks darkness, indicating still intact thylakoid membranes. These results explain the shorter survival times of polar diatoms with increasing water temperatures during prolonged dark periods.