A field enhanced flow reactor using bias assisted photocatalysis was developed for bacterial disinfection in lab-synthesized and natural waters. The reactor provided complete inactivation of contaminated waters with flow rates of 50 mL/min. The device consisted of titanium dioxide nanotube arrays, with an externally applied bias of up to 6 V. Light intensity, applied voltage, background electrolytes and bacteria concentration were all found to impact the device performance. Complete inactivation of Escherichia coli W3110 (~ 8 × 103 CFU/mL) occurred in 15 sec in the reactor irradiated at 25 mW/cm2 with an applied voltage of 4 V in a 100 ppm NaCl solution. Real world testing was conducted using source water from Emigration Creek in Salt Lake City, Utah. Disinfection of natural creek water proved more challenging, providing complete bacterial inactivation after 25 sec at 6 V. A reduction in bactericidal efficacy was attributed to the presence of inorganic and organic species, as well as the increase in robustness of natural bacteria.