A kinetic model for the biodegradation of hazardous organic compounds involving intermediate formation in a soil-slurry system was developed. The model included sorption and desorption of a model compound (phenanthrene) and its intermediate (1-hydroxy-2-naphthoate), and their utilization by microorganisms as a primary substrate in the dissolved phase. Simulation results with one-step (complete degradation) and two-step (intermediate formation) models demonstrated how different kinetics of mass transfer and intermediate degradation lead to rate-limiting patterns in the phenanthrene biodegradation. Intermediate formation in the two-step model caused a delay in phenanthrene degradation, cell growth and CO₂ production compared to the one-step model. Slow biodegradation of intermediate made lag time longer, while slow mass transfer decreases phenanthrene degradation rate in the cell growth phase. Reverse phenomena, faster initiation of biodegradation with decreasing mass transfer rate, were found in the two-step model, which resulted from delays of intermediate sorption. The soilslurry modeling involving intermediate formation and mass transfer provides tools describing various phenomena such as extensions of lag time, delays of biodegradation in the later period, low cell yields, and particular relationships between initial substrates and intermediates.