The oxidation of bromoxynil and trifluralin was investigated using ozone (O 3) and O 3 combined with hydrogen peroxide (H 2O 2) in natural waters using batch reactors. The results indicated that these pesticides could not be completely degraded during ozonation, achieving degradation levels lower than 50%. An enhancement of the level of degradation was observed using O 3/H 2O 2 process. A biphasic behaviour of O 3 was also observed. Depending on the experimental conditions, the rate constant for O 3 decomposition was estimated to be between 7.4 × 10 −4 s −1 to 5.8 × 10 −2 s −1, and 3.2 × 10 −3 s −1 to 4.2 × 10 −2 s −1 for bromoxynil and trifluralin samples, respectively. Acute toxicity analysis performed using Microtox ® showed a decrease in the toxic effects of the samples on the luminescent bacteria during the first few minutes of treatment, followed by an increase of the toxic effects at the end of the reaction for both pesticides. The quantification of oxidation by-products generated during treatment was also addressed. The total molar balances of the degradation by-products versus the initial pesticide concentrations ranged from 60 to 103% under different experimental conditions.