The Belgian part of the North Sea (BPNS) is subjected to multiple environmental stressors. The impact of these stressors includes the modulation of fatty acid (FA) composition of the zooplankton. This study recorded temporal and spatial patterns of the FA profiles of two dominant calanoid copepods within the BPNS: Temora longicornis (Muller, 1785) and Acartia clausi (Giesbrecht, 1889). By means of distance-based linear modelling and by applying multi model inference to generalized additive models, environmental stressors were linked to patterns of the FA profiles of these species. The FA profiles of A. clausi and T. longicornis showed distinct intraspecific, spatial and temporal differences within the BPNS. Temperature and algal food quality (marked by the ratio of silicate concentration to dissolved inorganic nitrogen concentration, SiO4/DIN) were the most important drivers of seasonal fluctuations in the DHA/EPA ratio of both species. DHA/EPA ratio can be used as marker for stress in copepods in the BPNS in order to have a quick indication of food quality changes at the basis of the food web.