Chemical pollution is one of the global anthropogenic factors accelerating the decline of biodiversity. Current methods for environmental monitoring and assessment primarily focus on chemical and ecological measurements, with limited exploration of their interaction, specifically the biological impact. The assessment of chemical status does not ensure compliance with the description provided in Descriptor 8 of the Marine Strategy Framework Directive (MSFD), which outlines the essential requirements for achieving good environmental status of marine ecosystems. Existing EU regulations, such as the MSFD and the Habitats Directive, are already undergoing review, emphasizing the need for integrated chemical and biological monitoring and assessment systems. In order to uncover the potential of integrating chemical-biological monitoring, this dissertation research will investigate the impact of chemical pollution on aquatic ecosystems, particularly on species health. Studies will be conducted using Atlantic salmon and sea trout as model species to evaluate their suitability for chemical-biological monitoring, assuming that these migratory fish exhibit a high potential to reflect cumulative and synergistic environmental pollution effects. The investigation of fish will encompass cytogenetic, biochemical, hematological, population parameter, and biological biomarker analyses to assess their health during the spawning migration period. To identify individuals and monitor changes in the studied biomarkers over time, captured individuals will be tagged with internal radio-frequency identification (RFID) markers. The study aims to detect early genetic biomarker signals of environmental pollution effects, conduct comparative analyses of these biomarker responses in fish from various rivers in Lithuania, and establish baseline levels of cytogenetic biomarkers in salmonid fish species. These investigations have the potential to promote the integration of biological effect assessment into the monitoring programs of aquatic ecosystems, thereby enhancing our comprehension of the cause-and-effect relationships between environmental pollution, biodiversity alterations, and ecological conditions. The research findings can serve as a foundation for the implementation of novel criteria, the formulation of practical recommendations for biological effects assessment, and the advancement of methodologies for evaluating the status of aquatic ecosystems.