This work summarizes important information about microalgae and nanoparticles. It deals with the possible mechanism of the effect of nanoparticles, describes some of the most used nanoparticles and summarizes available information on their toxic impact on algae. The main research part deals with the influence of nanoparticles on the secondary metabolism of uni-cellular microalgae, focused mainly on phenolic compounds and their role in the antioxidant response of microalgae. The level of oxidative stress was investigated by evaluating biomass growth, total antioxidant capacity and concentration changes of compounds involved in the glutathione-ascorbate cycle. This work also focused on carotenoids, chlorophylls, vitamins, that play an important role as antioxidants, and substances of the methionine cycle. Total quantities of flavonoid compounds and polyphenols were determined by spectrophoto-metric method. The same method was also used to monitor algal growth, total antioxidant capacity, chlorophyll and carotenoid content. The content of individual phenolic compounds, as well as the vitamins and compounds of glutathione-ascorbate and methionine cycles, was determined by liquid chromatography with mass spectrometry detection.