We investigated the bioaccumulation of metals (Cd, Se, and Zn) in different juvenile sizes of black sea bream Acanthopagrus schlegeli by applying a biokinetic model. A series of experiments were conducted to determine the physiological kinetic parameters, including uptake rate constant of waterborne metals, ingestion rate, assimilation efficiency of dietary metals, efflux rate constant, and specific growth rate as a function of fish size. Body concentration of metals as a function of body size was then simulated by the kinetic model and compared with the actual measurements. The uptake rate constants decreased with increasing fish size, with an allometric exponent (b) of 0.615 to 0.662. Ingestion rate was also negatively correlated with the fish size (b = −0.604). Assimilation efficiencies of Cd were independent of body size, whereas those of Se and Zn increased with fish size. In contrast, efflux rate constants and growth rate constants for metals were comparable in different sizes of fish. Predicted concentrations of Cd and Zn were comparable to actual measurements and were negatively correlated with fish size. Ingestion rate was the most important parameter accounting for the size-dependent bioaccumulation of metals, followed by dietary assimilation. We further showed that the trophic transfer potentials of Se and Zn were >1 in smaller fish but then reduced to <1 in larger ones, suggesting that trophic transfer potentials are highly size dependent in marine fish.