The acute toxicity of CuO and ZnO nanoparticles in artificial freshwater (AFW) and in natural waters to crustaceans Daphnia magna and Thamnocephalus platyurus and protozoan Tetrahymena thermophila was compared. The L(E)C50 values of nanoCuO for both crustaceans in natural water ranged from 90 to 224 mg Cu/l and were about 10-fold lower than L(E)C50 values of bulk CuO. In all test media, the L(E)C50 values for both bulk and nanoZnO (1.1–16mgZn/l)were considerably lower than those of nanoCuO. The naturalwaters remarkably (up to 140-fold) decreased the toxicity of nanoCuO (but not that of nanoZnO) to crustaceans depending mainly on the concentration of dissolved organic carbon (DOC). The toxicity of both nanoCuO and nanoZnO was mostly due to the solubilised ions as determined by specific metal-sensing bacteria.