Water flea (Daphnia magna Straus, 1820) is a planktonic crustacean used as a model organism in validated methods in ecotoxicology research. In this research, we used water flea as a test organism to assess ecotoxicity of gold and silver nanoparticles stabilized with thiol biomolecules (gluthatione and/or cysteine). We compared the effects of gold and silver nanoparticles with ecotoxicological effects of their ionic forms (Ag+ and Au3+). Besides determining the survival of water fleas after the treatment with nano and ionic forms of gold and silver we, also measured levels of oxidative stress biomarkers (superoxide radical, peroxide radical and gluthatione) by using fluorescent probes dihydroethidium, dichloro-dihydro-fluorescein diacetate and monochlorobimane. The aim of this study was to ascertain whether thiol stabilization of gold and silver nanoparticles decreases their ecotoxicological effect. Results obtained in acute toxicity testing showed greater toxicity when water fleas were exposed to ionic forms of gold and silver than when exposed to nanogold and nanosilver. Ionic silver exhibited the greatest toxicity which goes in accordance with previous research. Gluthatione coating showed greater toxicity than cysteine coating. However, nanogold showed no toxicity whatsoever. Results obtained in reactive oxygen species (ROS) assay indicated oxidative stress in water fleas when exposed to each fluorescent probe. Ionic silver showed greater level of oxidative stress than ionic gold. Furthermore, the dynamics between superoxide and peroxide radical were observed when using probes dichloro-dihydro-fluorescein diacetate and dihydroethidium. Finally, nanosilver stabilized with gluthatione showed the greatest level of oxidative stress.