Industrial wastewater, secondary effluents of sewage treatment plants and run-off from agricultural fields are the major sources of aquatic and terrestrial environment pollution by a variety of toxic compounds. Usage of plant test species has proven essential in investigation, detection and quantification of toxicity in the natural environment. Duckweed (Lemna minor L.) is often used as a plant model because it is a widely spread monocot, multiplies rapidly and shows tremendous metal accumulating capacity. Effects of toxic compounds present in chosen surface waters (Sava Županja, Sava Jesenice, Sutla Prišlin, Krapinica Krapina, Toplica downstream from Daruvar, Kutinica before confluence in Ilova, Glogovnica Mostari, lake Kozjak (taken every month during 3 months) and waste waters (ZGOS taken every 4 hours during 24 hours, Jakuševac and Gorjak taken once) on membrane lipids were investigated using duckweed as a plant test system. Plant material was harvested after 7-day exposure. Indicator of lipid peroxidation, malondialdehyde content, considerably increased in all wastewaters and in surface waters Sutla Prišlin, Kutinica and lake Kozjak. Use of primary producers for testing surface and waste waters in combination with physical and chemical analysis, can be good indicator of the environment pollution. Results obtained in this work indicate the presence of toxic compounds in surface and waste waters that may impact aquatic ecosystem but also present potential risk to all living organisms. Results also show that malondialdehyde content is a reliable indicator of toxicity and could be used in the biomonitoring of surface and wastewaters.