In this study, total organic carbon (TOC) biodegradation was simulated by GPS-X software in biofilm reactors with carriers of plastic rings and glass beads under different hydraulic conditions. Hydrodynamic model by retention time distribution and biokinetic measurement by in-situ batch test served as two significant parts of model calibration. Experimental results showed that TOC removal efficiency was stable in both media due to the enough height of column, although the actual hydraulic volume changed during the variation of hydraulic condition. Simulated TOC removal efficiencies were close to experimental ones with low theil inequality coefficient values (below 0.15). Compared with glass beads, more TOC was removed in the filter with plastic rings due to the larger actual hydraulic volume and lower half saturation coefficient in spite of its lower maximum specific growth rate of biofilm, which highlighted the importance of calibrating hydrodynamic behavior and biokinetics.