Nanoparticles of TiO2 and CuO are among most commonly used nanoparticles, and elevated concentrations of them are expected to be found in all environments, including aquatic. A standard growth inhibition test ISO/CD 20079 was used to determine the toxicity of nano sized and larger micro sized (bulk) particles in the concentrations of 0.1, 1, 10, 100 and 1000 μM CuO and TiO2 on common duckweed (Lemna minor L.). Both nano and bulk CuO particles caused changes in the structure and function of treated plants. The number of fronds and colonies decreased by as much as 78%, the length of roots and fronds decreased by 99% and 14%, respectively. Furthermore, photochemical efficiency was reduced by up to 35%, and the activities of antioxidative enzymes guaiacol peroxidase, ascorbate peroxidase and glutathione reductase increased by more than 240%. The altered physiological state of the CuO exposed plants was also reflected in the elevated occurrence of necrosis and bleaching in the duckweed colonies. Nano sized particles of CuO proved more phytotoxic than bulk particles, and the effects of both studied CuO sizes were concentration dependent. On the other hand, both bulk and nano sized particles of TiO2 caused no severe phytotoxic effects, there was no concentration dependence and they could be considered as non-harmful to common duckweed.