The purpose of this research was to study the disinfection of sanitary effluent from constructed wetlands, evaluating the oxidation of organic matter, the formation of formaldehyde, as well as the efficiency of total coliforms and Escherichia coli inactivation. A constant flow of ozone was applied to the batch system in 5 and 10 mg.O3 L−1 doses with contact times of 5 and 10 min. This study revealed that the average values of formaldehyde formation ranged between 259.00 and 379.00 μg L−1, which means that the values are within World Health Organization recommended values. The total coliforms and E. coli showed complete inactivation in almost all tests. The dose of ozone 5 mg.O3 L−1 and contact time of 5 min were sufficient for a significant reduction of the concentration levels of pathogens in constructed wetlands effluent with similar characteristics, thus allowing for its agricultural reuse.