Heavy metals in air, soil, and water are great threat to the environment. Effluents from paint, tannery, electroplating industries contaminate irrigation water, which in turn exhibit toxic response to many crops and microorganisms including cyanobacterial biofertilizers. In aquatic system Cr exist in many forms, whereas, Cr(VI) is most toxic. In the present study metabolic alteration were studied in a cyanobacterial biofertilizer (Hapalosiphon fontinalis) in response to chromium (VI) with special reference to oxidative stress. Maximum growth inhibition was observed at 0.5 mM Cr at 20th day. Lipid peroxidation as TBARS increased with the increase in chromium concentration and suggested free radical mediated toxicity. Elevated levels of β- carotene, astaxanthin, superoxide dismutase, catalase and ascorbate peroxidase indicated their role in survival strategy of the test organism.