This study was conducted to deepen our current knowledge on the possible negative effects which chlorpyrifos (CPF) and cypermetrin (CYP) could have on the lysosomal membrane stability (LMS) and enzymatic activity of cholinesterase (ChE), catalase (CAT) and glutathione peroxidase (GPx), using the invasive mollusk zebra mussel (Dreissena polymorpha) as bioindicator. The assessment of sentinel species aims to provide valuable information regarding the anthropogenic impact on aquatic ecosystems. The mussels were exposed to different decreasing concentrations of CPF and CYP in laboratory conditions for 96 hours (acute exposure) and 31 days (chronic exposure). The applied pesticides are considered as priority substances in surface waters according to Directive 2013/39/EU. Furthermore, lysosomal alterations are recognized as biological tools for determination of the effects of marine contaminants and implementation of the environmental quality standards (EQSs) specified in the Descriptor 8 of the Directive 2008/56/EC (MSFD). Alterations in the specific enzymatic activity could also be used as a sensitive biomarker for the examining the toxic stress in the hydrobionts subjected to various pollutants in water. The results showed changes in the lysosomal membrane destabilization, as well as in the specific enzymatic activity of ChE, CAT and GPx. However, the CYP exposure led to more pronounced alterations in the observed biomarkers.