The effect of lead and copper on apical segments of Gracilaria domingensis was examined. Over a period of 7 days, the segments were cultivated with concentrations of 5 and 10 ppm under laboratory conditions. The samples were processed for light, confocal, and electron microscopy, as well as histochemistry, to evaluate growth rates, mitochondrial activity, protein levels, chlorophyll a, phycobiliproteins, and carotenoids. After 7 days of exposure to lead and copper, growth rates were slower than control, and biomass loss was observed on copper-treated plants. Ultrastructural damage was primarily observed in the internal organization of chloroplasts and cell wall thickness. X-ray microanalysis detected lead in the cell wall, while copper was detected in both the cytoplasm and cell wall. Moreover, lead and copper exposure led to photodamage of photosynthetic pigments and, consequently, changes in photosynthesis. However, protein content and glutathione reductase activity decreased only in the copper treatments. In both treatments, decreased mitochondrial NADH dehydrogenase activity was observed. Taken together, the present study demonstrates that (1) heavy metals such as lead and copper negatively affect various morphological, physiological, and biochemical processes in G. domingensis and (2) copper is more toxic than lead in G. domingensis.