The biomagnification of metals (Cd, Co, Cr, Cu, Fe, Mn, Pb and Zn) and the metalloid As in aquatic systems is a global health concern. In this study, concentrations of fatty acid biomarkers in zooplankton were analyzed from the Pearl River, South China between September 2016 and July 2017. The objective was to examine how particulate matter, algae and bacteria food sources affect metal bioaccumulation using fatty acid facilitation. In the zooplankton fraction, positive correlations were observed between Pb concentration and Eicosapentaenoic acid (EPA), Zn and Docosahexaenoic acid (DHA) (diatoms and Cryptophyceae biomarkers), Fe with Palmitoleic acid (C16:1n-7, diatom marker), and a weak association of Mn with α-linolenic acid (C18:3n-3). Cu concentration in the zooplankton increased significantly with an endogenous biotic biomarker Stearic acid (C18:0, bacteria biomarker), while Cd concentrations increased with increasing Oleic acid (C18:1n-9, green alga biomarker) concentration. There was a positive correlation between Cr concentration and the sum of Pentadecylic and Margaric acids (C15:0 + C17:0, bacteria biomarkers). Seven of the nine metals examined showed associations with fatty acids in the zooplankton. The bioaccumulation of Co, Cu, Pb, Fe, Mn and Zn concentration was correlated to the individual biomasses of Brachionus calyciflorus, Filinia longiseta, Schmackeria forbesi, Limnoithona sinenisis, Thermocyclops brevifurcatus, and Diaphanosoma dubium. For selected zooplankton taxa, the algal biomasses of Euglenophyceae, Chlorophyceae, Cryptophyceae, and Bacillariophyceae were correlated. Zooplankton were affected by selected species of phytoplankton and bacteria numbers in the Pearl River. These results show that metal accumulation in zooplankton is not only correlated with diet but is also in part, species specific with metal type. Thus, the bioaccumulation or scavenging of metals across trophic levels is a fundamental and complex component of metal cycling in aquatic environments.