Process control parameters influencing microbial perchlorate reduction via a flow-through zero-valent iron (ZVI) column reactor were investigated in order to optimize perchlorate removal from water. Mixed perchlorate reducers were obtained from a wastewater treatment plant and inoculated into the reactor without further acclimation. Examined parameters included hydraulic residence time (HRT), pH, nutrients requirement, and perchlorate reduction kinetics. The minimum HRT for the system was concluded to be 8 hr. The removal efficiency of 10 mg·L^-1 influent perchlorate concentration was reduced by 20%–80% without control to the neutral pH (HRT= 8 hr). Therefore pH was determined to be an important parameter for microbial perchlorate reduction. Furthermore, a viable alternative to pH buffer was discussed. The microbial perchlorate reduction followed the first order kinetics, with a rate constant (K) of 0.761 hr^-1. The results from this study will contribute to the implementation of a safe, cost effective, and efficient system for perchlorate reduction to below regulated levels.