Copper (Cu) in the form of copper sulfate (CuSO4) and copper oxide nanoparticles (CuO NP), arising mainly from agro-industrial activities, is known to have an adverse impact on algae. This study aimed to compare the toxicity of CuSO4 and CuO NP in Chlorella sp., which was isolated from a farmland in Cameron Highlands, Malaysia. Toxicity testing (96 h) based on chlorophyll-a concentration was conducted on cultures grown in Bold’s Basal Medium (BBM) added with CuSO4 ranging from 0 (control) to 200 μM or CuO NP ranging from 0 to 2 mM. In addition, the effects of CuSO4 and CuO NP at EC10 and EC50 on the pigmentation, oxidative stress response, and cell morphology of Chlorella sp. were assessed. Results showed that Chlorella sp. was more sensitive to CuSO4 (EC50 = 150 μM) than CuO NP (EC50 = 1.30 mM). Exposure to CuSO4 at EC50 but not CuO NP reduced the chlorophyll-a, chlorophyll-b, and carotenoid contents of the algal cells. At 96 h, CuSO4 at EC50 induced significant increase in the production of reactive oxygen species (ROS) and degree of lipid peroxidation. Agglomerates of nanoparticles and algal cells were seen in cultures treated with CuO NP, whereas clumping of cells occurred in cultures exposed to CuSO4. Some CuO NP were found to penetrate the cell wall and be internalized into the algal cells. In conclusion, the toxicity of CuSO4 and CuO NP in Chlorella sp. differed in terms of their effects on growth, pigmentation, and oxidative stress response.