The objective of this research article is to present the results of the evaluation of a pilot unit for microorganism reduction in urban wastewater using the hydrodynamic cavitation (HC) principle, which was developed by the San Gil University Foundation (UNISANGIL). Three hydrodynamic cavitation reactors (HCRs), named CAV-A, CAV-2A, and CAV-2V, were tested in the designed disinfection system. The experiments evaluated each reactor in terms of the logarithmic reduction (LR) and the percentage reduction (Pr) for four microbiological parameters: fecal coliforms, total coliforms, aerobic mesophilic and molds and yeasts, during the treatment of urban wastewater discharged into a natural point of the Fonce River in San Gil, Santander, Colombia. Three tests were performed on each reactor in a system with a flow rate of 10L/s and a tank of 1800L. The results for the reactor of the best performance (Venturi type, CAV-V) were, on average for each parameter, 0.68±0.31, 0.69±0.15, 1.57±1.09 and 0.9±0.09 for LR, and 74±13.83, 78±7.87, 89±9.68, and 87±2.57, for Pr. This work is a pioneer in developing microorganism reduction in wastewater of an actual discharge over a river without a previous primary and secondary treatment. Experiments demonstrate the viability of applying HC as an alternative physic element for the tertiary treatment of urban wastewater, especially in continuous flow scenarios prior to discharge. This study's findings could significantly impact how we approach wastewater treatment in urban areas. Further research is needed to validate the system's efficiency in combination with other disinfection methods.