The aim of this study was to investigate the influence of specific environmental factors, such as temperature, pH, oxygen concentration, and phosphate, nitrate, chloride, sodium, potassium, sulphate, magnesium and calcium ions concentration, as well as microcystins, on the seasonal variations in the activity of the antioxidant system of the zebra mussel. We examined changes in lipid peroxidation (LPO) levels, glutathione content and the catalase activity of mussels inhabiting the two ecosystems, which differ due to their trophic structure and the presence of toxic cyanobacteria. The results show a relationship between the activity of the antioxidant system of zebra mussels and the seasonal fluctuations of environmental parameters: the symptoms of oxidative stress were generally the highest during spring and the lowest during summer in both ecosystems. Our study also revealed that regardless of the study area the most important factors determining the activity of the antioxidant defences of mussels were the mineral composition (particularly magnesium and calcium ions concentrations) and physical parameters of the water (oxygen concentration and pH). However, factors resulting from the trophic status of studied ecosystems, such as limitations in food resources or high concentration of microcystins during cyanobacterial blooms, were periodically responsible for increased level of LPO in the tissues of zebra mussel. These findings may indicate a limited tolerance of the zebra mussel to the local environmental conditions.