Copper and lead, as remnants of industrial activities and urban effluents, have heavily contaminated many aquatic environments. Therefore, this study aimed to determine their effects on the physiological, biochemical, and cell organization responses of Hypnea musciformis under laboratory conditions during a 7-day experimental period. To accomplish this, segments of H. musciformis were exposed to photosynthetic active radiation at 80 μmol photons m(-2) s(-1), Cu (0.05 and 0.1 mg kg(-1)), and Pb (3.5 and 7 mg kg(-1)). Various intracellular abnormalities resulted from exposure to Cu and Pb, including a decrease in phycobiliproteins. Moreover, carotenoid and flavonoid contents, as well as phenolic compounds, were decreased, an apparent reflection of chemical antioxidant defense against reactive oxygen species. Treatment with Cu and Pb also caused an increase in the number of floridean starch grains, probably as a defense against nutrient deprivation. Compared to plants treated with lead, those treated with copper showed higher metabolic and ultrastructural alterations. These results suggest that H. musciformis more readily internalizes copper through transcellular absorption. Finally, as a result of ultrastructural damage and metabolic changes observed in plants exposed to different concentrations of Cu and Pb, a significant reduction in growth rates was observed. Nevertheless, the results indicated different susceptibility of H. musciformis to different concentrations of Cu and Pb.