Mediterranean barbel (Barbus meridionalis) an endemic species is currently facing habitat destruction and pollution in Osor River (Spain) due to mining runoff that has severely deteriorated the water quality by metals, primarily zinc (Zn). In order to assess the potential risk of metal contamination and hydrological changes in the Osor River by using oxidative stress and neurotoxicity biomarkers via IBR analyses in the barbel, five different stations were chosen: upstream (S1: reference site and S2: hydrologically changed), mine (S3), and downstream (S4 and S5). The highest tissue metal levels were measured particularly at S3 and following downstream sites. SOD activity and the GSH system parameters (GPX, GST, and GSH) were the most sensitive oxidative stress indicators among the antioxidant system parameters. The organs with the greatest changes in antioxidant biomarkers were the liver and gill. As a sign of neurotoxicity, AChE activities significantly raised in the brain and muscle but drastically lowered in the kidney, liver, and gill particularly in the area of mine and downstream compared to reference site. Integrated biomarker response index (IBR) method was applied to visualize the affect of metal and hydrological alterations with biomarker response according to sites in the Osor River. IBR analyzes together with correlations between metal levels and oxidative stress biomarkers, emphasized that S2 and S3 have the greatest impact on the biomarker levels due to mine activity and hydrological changes highlighting the vulnerability to extinction of native fish B. meridionalis. It is also critical to assess the current data based on the multi-biomarker approach for a range of detrimental effects on fish fitness at the individual level as well as population persistence from an ecological standpoint.