A 30 kV pulsed power treatment system was designed and developed to process fluid materials. Our objective was to investigate the effects of high voltage electric pulses on microbial inactivation in an aqueous solution under different operating conditions and fluid properties. Electric field strength at 10 kV/cm for 10 pulses (2 sec pulse period and 2 μsec pulse width) with a spike of reverse polarity resulted in significant microbial control. P. fluorescens in various aqueous solutions were reduced in population by more than six log cycles. However, the critical electric field strength was affected by the nature of the pulse waveform across the treatment chamber which, in turn, was a function of electrode distance and fluid properties. Sudden charge reversal immediately at the end of a pulse provided maximum microbial decay.