Steroids have attracted particular attention as environmental contaminants because of their severe endocrine-disrupting effects. Previous studies have predominantly focused on parent steroids; however, the levels and proportions of the free and conjugated forms of their metabolites remain largely unclear, especially in food webs. Here, we first characterized the free and conjugated forms of parent steroids and their metabolites in 26 species in an estuarine food web. The steroids were dominated by their metabolites in water samples, whereas parent compounds were predominant in sediment samples. The total mean steroid concentrations in the biota samples that underwent non-enzymatic hydrolysis decreased in the following order: crabs (27 ng/g) > fish (5.9 ng/g) > snails (3.4 ng/g) > shrimps and sea cucumbers (1.2 ng/g); and those in the biota samples that underwent enzymatic hydrolysis decreased in the following order: crabs (57 ng/g) > snails (9.2 ng/g) > fish (7.9 ng/g) > shrimps and sea cucumbers (3.5 ng/g). The proportion of metabolites in the enzymatic hydrolysis biota samples was higher (38−79%) than that (2.9−65%) in non-enzymatic ones, indicating that the free and conjugated forms of metabolites in aquatic organisms were not negligible. Most synthetic steroids were either bioaccumulative or highly bioaccumulative. Importantly, in the invertebrate food web, 17α-methyltestosterone was biomagnified, while 17β-boldenone underwent trophic dilution. Although the estuarine water had a median ecological risk level, the health risks via aquatic product consumption were very low. This study provides novel insights into the composition and trophic transfer of steroids in an estuarine food web for the first time and highlights that free and conjugated metabolites should receive more attention, particularly in biota samples.