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Lacustrine ecosystems have been altered by accelerating pollution, excessive nutrient and organic load, water abstraction, and are susceptible to climate change. Hence, suggesting sensitive and reliable biomarkers for early assessments of their status is of urgent need. In this study, two freshwater commercial fish species, Cyprinus carpio (carp) and Carassius gibelio (prussian carp) from two lakes (i.e. Koronia and Volvi, Northern Greece) with different anthropogenic pressures were used and a battery of biochemical and molecular biomarkers related to stress response were analyzed in fish gills and liver. In parallel, water physicochemical parameters (T, DO, pH, conductivity, salinity), BOD5 and nutrient (N-NO3, N-NO2, N-NH4, P-PO4) concentrations were measured. Results showed that Lake Koronia had higher conductivity and salinity values and N-NO(2 )concentrations. Levels of Heat Shock Response (HSR), MAPK phosphorylation, protein carbonylation, lipid peroxidation products, Bax/Bcl-2 ratio, ubiquitination and caspases were increased in gills and liver of both fish species sampled from Lake Koronia in relation to those of Lake Volvi. Likewise, liver lipid content was increased in both fish species sampled from Lake Koronia compared to those sampled from Lake Volvi. The results indicate and reflect the higher environmental degradation that prevails in Lake Koronia ecosystem in comparison to that of Lake Volvi. The fish species studied showed different susceptibility depending on the biomarkers examined. In addition, our results from both examined species provide insight into the mechanisms involved in acclimatization to stressful environments and support the role of the studied biomarkers as sensitive and reliable tools for ecological assessments of lake ecosystems in biomonitoring studies.