Abstract The biochemical composition and abundance variation of zooplankton (copepods and Artemia salina) were determined in four ponds of increasing salinity (A5, A16, C41 and M2) in the Sfax solar saltern (Tunisia). The zooplankton community was dominated by copepods in the ponds A5, A16 and C41. The pond M2 was marked by the presence of only Artemia salina. Our results showed the dominance of total saturated fatty acids (SFA), which made up 57%–95% of total fatty acids (TFA). SFA 16:0 and 18:0 dominate in all ponds. A. salina showed the highest amounts of the total monounsaturated (MUFA) and polyunsaturated fatty acids (PUFA), this indicates that this species could be employed in hatcheries and used as food source for some aquarium species. Fatty acids of herbivory, proportion of all diatom markers to all flagellate markers (D/F), were negatively correlated with the total zooplankton (r = −0.998, p < 0.05). A. salina was negatively correlated with a biomarker for carnivory polyunsaturated fatty acids/saturated fatty acids (PUFA/SFA) (r = −0.959, p < 0.05). The dietary quality of zooplankton seems to be dependent on food availability in the four studied ponds.