Seafloor massive sulfide (SMS) deposits are the target of available metallic resources. The toxic impacts of leachable metals from hydrothermal ore by mining operations in marine environments are a concern. However, ecotoxicological knowledge about marine algae, and particularly open ocean species, is still limited. Here, we evaluated the toxic effects of three leachable metals (i.e. Zn, Cu, and Pb) on seven marine algae, including cyanobacteria and eukaryotes, by a delayed fluorescence method. Cyanobacterial Synechococcus and Cyanobium species were sensitive to Zn and Cu, while eukaryotic algae showed various responses to heavy metal species. The prasinophycean Bathycoccus prasinos NIES-2670 was sensitive to all metal species; this strain is a potential test strain to detect the leachable metals. A co-culture experiment showed that the impact on community structure varies depending on leachable metal species. This study demonstrates that surveys across multiple taxonomic groups are necessary to assess the impact of SMS-mining operations on marine ecosystems as a whole.