The occurrence of toxic cyanobacteria in the aquatic environment constitutes a serious risk for the ecological balance and the functioning of ecosystems. The presence of cyanotoxins in ecosystems could have eventual adverse effects on aquatic plants, which play an important biological role as primary producers. The original aim of this study was to investigate microcystin (MC) accumulation, detoxication and oxidative stress induction in the free-floating aquatic vascular plant Lemna gibba (Duckweed, Lemnaceae). Experiments were carried out with a range of MC levels, obtained from toxic Microcystis culture extracts (0.075, 0.15, 0.22 and 0.3 microg equiv.MC-LR mL(-1)). During chronic exposure of the plant to MC, we examined the growth, photosynthetic pigment contents and also the physiological behavior related to toxin accumulation, possible biodegradation and stress oxidative processes of L. gibba. For the last reason, changes in peroxidase activity and phenol compound content were determined. This is a first report using phenol compounds as indicators of biotic stress induced by MC contamination in aquatic plants. Following MC exposure, a significant decrease of plant growth and chlorophyll content was observed. Also, it was demonstrated that L. gibba could take up and bio-transform microcystins. A suspected MC degradation metabolite was detected in treated Lemna cells. In response to chronic contamination with MCs, changes in the peroxidase activity and qualitative and quantitative changes in phenolic compounds were observed after 24h of plant exposure. The physiological effects induced by chronic exposure to microcystins confirm that in aquatic ecosystems plants coexisting with toxic cyanobacterial blooms may suffer an important negative ecological impact. This may represent a sanitary risk due to toxin bioaccumulation and biotransfer through the food chain.