Plankton fractions from a saline lake in Argentina were studied using a combined trophic marker approach. A strong seasonality of biomarkers was characteristic for the different fractions, particularly the variations in the 18:4(n - 3) and 20:4(n - 3) fatty acids and the δ13C values. The primary production in the lake was mainly driven by diatoms, reflected by the close relation of δ13C, chlorophyll a and diatom fatty acid markers. The combined approach of δ13C and 20:4(n - 3) enabled processes in the lipid metabolism of the copepod Boeckella poopoensis to be inferred. The polyunsaturated fatty acid 22:6(n - 3) and the δ15N separated the trophic levels in this food web with copepods at higher trophic level. Nutritional stress and omnivory of B. poopoensis partially explained the δ15N variations in mesozooplankton. The δ15N signature was probably driven by cyanobacteria in the microplankton and by microbial processes in the nanoplankton fraction. Warmer temperatures may favour the saturation of microalgae fatty acids and the abundance of plankton groups richer in saturated fatty acids. The tendency to unsaturation in mesozooplankton at colder temperatures was probably influenced by diet and metabolic requirements. Future temperature increase and eutrophication-like processes may increase the importance of cyanobacterial and bacterial markers under climate change scenarios.