The response of the freshwater microalga, Chlorella vulgaris, to heavy metal stress was examined based on chlorophyll fluorescence analysis to assess the toxic effects of heavy metals in freshwater ecosystems. When toxic effects were analyzed using regular chlorophyll fluorescence analysis, photosystem II activity(Fv/Fm) decreased significantly when exposed to Cu2+ and Hg2+ for 12 h, and decreased in the order of Hg2+ > Cu2+ > Cd2+ > Ni2+ when exposed for 24h. The effective photochemical quantum yield(Φ′PSII), chlorophyll fluorescence decrease ratio(RFd), minimal fluorescence yield(Fo), and non-photochemical quenching(NPQ), but not photochemical quenching(qP), responded sensitively to Hg2+, Cu2+, and Cd2+. These results suggest that Fv/Fm, as well as Φ′PSII, RFd, Fo, and NPQ could be used to assess the effects of heavy metal ions in freshwater ecosystems. However, because many types of heavy metal ions and toxic compounds co-occur under natural conditions, it is difficult to assess heavy metal toxicity in freshwater ecosystems. When Chlorella was exposed to heavy metal ions for 12 or 24h, Fv/Fm and maximal fluorescence yield(Fm) changed in response to Hg2+ and Cu2+ based on image analysis. However, assessing quantitatively the toxic effects of several heavy metal ions is challenging.