A simulated wastewater containing phenol (2500 mg/L), thiocyanate and ammonia-nitrogen (500 mg/L) was treated in an anaerobic (R1)–anoxic (R2)–aerobic (R3) moving bed biofilm reactor system at different hydraulic retention time (HRT) intervals (total HRT 3–8 days, R1: 1.5–4 days; R2: 0.75–2 days and R3: 0.75–2 days) and feed thiocyanate (SCN −) concentrations (110–600 mg/L) to determine substrate removal kinetics. In R1, phenol and COD reduction and specific methanogenic activity were inhibited due to the increase of SCN − in feed. Bhatia et al. model having inbuilt provision of process inhibition described the kinetics of COD and phenol utilization with maximum utilization rates of 0.398 day −1 and 0.486 day −1, respectively. In R2 and R3 modified Stover–Kincannon model was suitable to describe substrate utilization. In R2 respective maximum SCN −, phenol, COD and NO 3 −-N utilization rates were 0.23, 5.28, 37.7 and 11.82 g/L day, respectively. In aerobic reactor R3, COD, SCN − and NH 4 +-N removal rates were, respectively, 10.53, 1.89, and 2.17 g/L day. The minimum total HRT of three-stage system was recommended as 4 days.