Organophosphate flame retardants (OPFRs) can rapidly biotransform into two types of metabolites in biota: (1) organophosphate diesters (DAPs) and (2) hydroxylated OPFRs (HO-OPFRs). Therefore, the levels of parent OPFRs alone are not sufficient to indicate OPFR pollution in biological organisms. This study analyzed 12 OPFR metabolites, including 6 DAPs and 6 HO-OPFRs, in a typical freshwater food chain consisted of crucian carp, catfish, mud carp, snakehead, and oriental river prawn. The total concentrations of OPFR metabolites were comparable to those of parent OPFRs, and ranged from 0.65 to 17 ng/g ww. Bis(2-butoxyethyl) 3′-hydroxy-2-butoxyethyl phosphate (14%–77%), di-n-butyl phosphate (DNBP) (6.7%–24%), bis(1-chloro-2-propyl) phosphate (BCIPP) (0.7%–35%), and 1-hydroxy-2-propyl bis(1-chloro-2-propyl) phosphate (BCIPHIPP) (6.0%–24%) were the major OPFR metabolites. Various aquatic species exhibited significant differences in their OPFR metabolite/parent ratios (MPR) (p < 0.05), indicating varying biotransformation potentials of different organisms for various OPFRs. The growth-independent accumulation of tri-n-butyl phosphate (TNBP), tris(chloro-2-propyl) phosphate (TCIPP), triphenyl phosphate, and 2-ethylhexyl diphenyl phosphate in mud carps could be explained by their biotransformation potential. A significant negative correlation was found between the concentration of bis(2-butoxyethyl) phosphate and δ15N values (p < 0.05), with a calculated trophic magnification factor (TMF) of 0.66. Significant positive correlations were observed between BCIPP and TCIPP (R2 = 0.25, p < 0.05), as well as between DNBP and TNBP (R2 = 0.30, p < 0.01), implying that these two DAPs could be used as biomarkers to quantitatively assess TCIPP and TNBP contamination in wild aquatic organisms.