Freshwater invertebrates are commonly used in biological monitoring, but research of biomarkers at biochemical level is still at the early stage of development. Biomarkers in aquatic species are regarded as important for detecting stressor components, such as presence of pollutants and changes in environmental factors (pH, temperature, dissolved oxygen, etc.). In this study, to evaluate the pollution in Kocabaş Stream, we used specific biomarkers (GSH, TBARS and Na+, K+-ATPase) in homogenates of whole organisms. Macro invertebrate samples were sampled from three locations receiving increasing levels of urban and industrial waste water discharges along the Kocabaş Stream (Çanakkale-Turkey) in April and July 2013. Locations were selected to include the aquatic communities in poor and good ecological state depending on the measured physico-chemical water parameters and the analysis of benthic macro invertebrate communities. According to the results of the study, statistically important increases in TBARS and GSH level of Asellus aquaticus, Gammarus pulex pulex and Potamon ibericum collected from the stations in Çan and Biga were observed compared to the individuals collected from Yenice. These results indicated that presence of serious pollutants in Kocabaş Stream especially in Çan region also occurred in the physiology of macro invertebrate organisms living in the region.