L. marginalis is an important biological component of freshwater ecosystem and an efficient bioaccumulator of toxin residues. Being a filter feeder, this species performs biological filtration of ambient water and keeps the water body biologically safe for other species. Natural habitat of the species is under risk of contamination by multineeem, a newly introduced azadirachtin (limonoid) based pesticide. During monsoon, natural habitat of L. marginalis received residues of diverse xenobiotics along with azadirachtin. Reactive oxygen intermediates are major cytotoxic factor which is generated in invertebrates in diverse physiological conditions. The stimulation of superoxide anion production and resulting physiological damage is modulated by the presence of antioxidant enzyme namely superoxide dismutase (SOD) and catalase (CAT). Further the toxin residues are conjugated in gluthathione pool through glutathione-Stransferase (GST). This is a protective phenomenon in bivalves. In L. marginalis, the activity levels of antioxidant enzymes namely superoxide dismutase and catalase activites were significantly low than control in gill and digestive gland under toxin exposure respectively. In case of glutathione-S-transferase, azadirachtin moderately suppress the activity of the enzyme in selected tissues of L. marginalis. © 2014 by Nova Science Publishers, Inc. All rights reserved.