Diminishing water sources and their contamination by pathogenic microorganisms in pariculat set forth the neccessity of application of disinfection processes. Chlorine which has been used for disinfection purposes and disinfection by-products generated bu the reaction of chlorine with organic compounds are known to have adverse effects on human health, therefore the research on alternative disinfection techniques has brought into question. Ultrasound disinfection is among major alternative disinfection technologies. In this study the removal of Eschericia coli that is a major indicator microorganism which is a fecal contamination factor that can be found in water media, was performed in ultrasound reactor. Various frequencies were studied in ultrasound reactor and effects of various media ions (HCO3-, NO3-, SO4-2) and hydrogen peroxide and nitrogen gas fed to the system at various flow rates were examined. Optimum microorganism inactivation was attained when the operation frequency of the reactor is 28kHz. The increased concentration of SO4-2 and HCO3-ions added to the system favored the microorganism inactivation, however the presence of NO3- didn't change the inactivation yield of the ultrasound system