Background: A prerequisite for long-term survival of populations under multi-stress conditions is their capacity to set up efficient adaptive strategies. However, changes in the activity of molecular biomarkers have been for decades considered as early signals of the deterioration of the fish health and evidence of stress-related adverse biological effects. The aim of this study was to show that such changes actually represent adaptive response of fish to chemical stress. Gene expression and enzyme activity level in liver and brain of specimens from two populations of Abramis brama from contrasted habitats (nature reserve and urban) were examined. Selected parameters included biomarkers of general stress, antioxidative defence, xenobiotic metabolism, endocrine disruption, glucose homeostasis, iron homeostasis, and neurotoxicity. Results: Exposure of A. brama population from urban area to chemical stress was confirmed by assessment of chronic toxic pressure at fish habitats using Toxic Unit approach. The most pronounced response to chemical stress is observed through the activation of antioxidative defence mechanisms in brain and liver at gene and enzyme activity level, high biotransformation capacity of liver, and activation of mechanisms that will meet energy demands and compensate for the metabolic costs of the response to toxicants (higher expression of genes related to glucose homeostasis in the exposed population). Higher hepatosomatic index in the exposed population implies liver hypertrophy due to increased functional load caused by pollution. Body condition factors indicate good overall condition of both fish populations and confirm high efficacy of mobilized adaptation mechanisms in the exposed population. Conclusions: The study provided the first data on basal expression of a number of genes in A. brama, potentially valuable for biomonitoring studies in absence of clear pollution gradient and/or reference sites (conditions). The study highlights importance of newly identified roles of various genes and proteins, typically considered as biomarkers of effects, and shows that changes in these parameters do not necessarily indicate the deterioration of the fish health. Such changes should be considered as adaptive response to chemical stress, rather than direct proof of ecological impact of pollution in situ.