The Basic blue 3 dye is a cationic dye gives colour shading from blue to green by addition with different chemicals. The acute exposure of this dye for 96 hours to bivalves showed altered physiological parameters. Increased level of antioxidant enzymes in gill, hepatopancreas, gonad and mantle of bivalve was recorded. At 70 ppm concentration of Basic blue 3 dye showed significant increase in gill and hepatopancreas while non-significant increase in gonad and mantle. At both the concentration 40 ppm and 70 ppm of the dye gives structural changes in gill, hepatopancreas and gonad assessed by histology. In gill, the structural changes were Swollen gill lamellae, ruptured epithelial cells, disorganization of gill filament and cell necrosis noticed; the hepatopancreas showed the abnormal shape of digestive tubules, destruction of digestive cells, mixing of cellular content of tubules, damages at basement membrane and degeneration of connective tissue while in gonad Stages of oocytes showed degenerative changes, the vacuolization in oocytes, degeneration of oolemma and ooplasm was observed. By comet assay tail DNA% and tail moment was recorded. At 70 ppm concentration, the gill cells showed significant tail DNA% and tail moment.