This research was conducted to investigate whether sequential anoxic/aerobic biofilm reactors and microfilteration (MF) membrane system can be used as a direct treatment for the removal of perchlorate and nitrate in groundwater. The biofilm process consisted of an anoxic first stage to remove perchlorate and nitrate and aerobic second stage to remove remaining acetate used as a carbon source for dissimilatory reduction of perchlorate and nitrate. In final stage, hollow fiber MF membrane was used to remove turbidity. In this research, perchlorate was reduced from the influent concentration of 102 ${mu}/L$ to below the IC detection level (5 ${mu}/L$) and nitrate was reduced from 61.8 mg/L (14 mg/L $NO_3$-N) to 4.4 mg/L (1 mg/L $NO_3$-N). Acetate used as a carbon source was consumed from 179 mg/L $CH_3COO-$ to 117 and 11 mg/L $CH_3COO^-$ in effluents from anoxic and aerobic biofilm reactors, respectively. Turbidity was reduced from 3.0 NTU to 1.5, 0.3, and 0.2 NTU in effluents from anoxic/aerobic biofilm reactors and MF membrane, respectively. It is expected that the sequential anoxic/aerobic biofilm reactors and MF membrane system can efficiently remove perchlorate and nitrate in surface water or groundwater.