In this study, the effects of different copper’s forms, metal salt (Cu2+), nano-metal (nano-Cu) and nano-metal oxide (nano-CuO), were tested on two marine algae named Skeletonema costatum and Nitzschia closterium. During a 96-hour exposure to nanoparticles (NPs) and salt, cell number, Cu2+ concentration in the culture medium, morphology and intracellular amino acids was measured to assess the toxicity of those copper materials and the toxicity mechanism of NPs. It was found that the toxicity of Cu2+, nano-Cu and nano-CuO on marine phytoplankton decreased in order. The EC50 values of Cu2+ and nano-Cu for S. costatum and N. closterium ranged from 0.356 to 0.991 mg/L and 0.663 to 2.455 mg/L, respectively. Nano-Cu inhibited the growth of marine phytoplankton mainly by releasing Cu2+, however, nano-CuO mainly produced toxic effects on microalgae through the effect of NPs. The secretion of extracellular polymeric substances by microalgae could be another possible reason for nano-Cu and nano-CuO to impose implications for microalgae. S. costatum was more sensitive to copper than N. closterium. Cu2+, nano-Cu and nano-CuO all reduced the total output of algae-derived amino acids by affecting the growth of phytoplankton and per-cell amino acids. This manuscript is of important implications to fill the data gaps for nano-Cu and nano-CuO risk assessment on marine algae.