The paper examined changes in the activity of Class III Peroxidase (POX) and polyphenol oxidase (PPO) in Phragmites australis (Cav.) Trin. Ex Steud. Utricularia vulgaris L. and Salvinia natans (L.) from two sites on Bardača wetland during one vegetation season (June-September). The results showed differences in POX and PPO activities between emergent, submersed and floating plants, depending on both the sampling period and the site. The obtained differences in enzyme activities are probably a reflection of the influence of different types of abiotic stress on plants in their natural habitat, but also specific adaptive characteristics of each of the investigated species. The obtained results indicate that the activities of POX and PPO in examined water macrophytes can be used as bioindicators of environmental conditions.