The influence of pH and substrate shocks was investigated on the performance of anaerobic reactor for simultaneous sulfide and nitrate removal. The performance was noticeably affected by the transient pH or substrate shocks. Unlike substrate shocks, the reactor was more sensitive to pH shocks. The effluent sulfide concentration was a sensitive parameter, which increased up to 31 times of that at steady state, so it could be used as an indicator of the reactor performance. The performance recovered from the disturbances during all the shocks applied. The recovering velocity was relatively stable, which did not increase with the increasing intensity of the shocks. The reactor was easier to recover from pH shocks than substrate shocks.