Scenedesmus rotundus was isolated from metal contaminated petroleum industry effluent and its tolerance to Cadmium and Zinc was tested using different concentrations of CdCl2 and ZnCl2 ranging from 0.001 mM to 1.0 mM of Cd and 0.03 mM to 1.21 mM of Zn amended in Bolds Basal medium. The changes in cell count recorded at regular intervals upto a period of 24 days revealed a concentration dependent inhibition in growth. Concentration of the metal, at which 50% of the cells are live and metabolically active referred to as EC50 was calculated as 0.04 mM for Cd and 0.2 mM for Zn. Further, the effect of EC50 of the metals on the protein content, uptake of metals at varying pH, oxidative stress markers including lipid peroxidation, protein oxidation andnd oxygen uptake, levels of enzymatic antioxidants such as catalase and superoxide dismutase and non-enzymatic antioxidants namely, GSH and PC4 were determined. Though a direct correlation could not be drawn between pH and metal uptake, the compartmentalization of the metal during the lag phase and exponential phase was evident, most of the metal was present in extracellular fractions in the former, while in the later it was internalized. Our study shows a clear correlation between toxicity of Cd and the ability of the algae to synthesize PC4 from GSH and chelate it leading to detoxification, while Zn treatment led to an increase in the activity of catalase and superoxide dismutase and replete GSH pools. Further the changes in the cell wall structure at EC50 of Cd and Zn were studied. This is the first report on effect of heavy metals on the structural modifications of the cell wall of Scenedesmus in general and Scenedesmus rotundus in particular, indicating appearance of granules on the entire cell surface in both Cd and Zn treatments, with the degree of granulation increasing in the order of pH 12 > 10 > 8 in Cd treatment. Further structures of higher order resembling minute wheels are observed in Cd treated cells are also reported.