Anthropogenic and climate factors increase the frequency of problematic cyanobacterial blooms in freshwater. Among other toxins, some cyanobacteria produce microcystins (MCs), which inhibit phosphatases type 1 and type 2A and provokes oxidative stress. Toxic cyanobacteria affect the growth, survival and reproduction of zooplankton, particularly those from the genus Daphnia, which have a central position in pelagic food webs. However, one possibility to ameliorate effects is to biotransform MC via glutathione S transferase (GST) to a less toxic glutathione conjugate. This process was hypothesised to underlie the ability of Daphnia to withstand MC and to explain the enhanced tolerance of the offspring from mothers exposed to toxic cyanobacteria. Thus we conducted multigenerational experiments with D. magna, exposing the parental generation to MC for 1 or 7 days and determining the enzyme-mediated tolerance to MC in their offspring by assessing the acute effect of MC on biotransformation and antioxidant and metabolism enzymes, and through 21day chronic tests on toxicity and growth. Seven days of exposure of the parental generation to MC induced higher activity of GST and malate dehydrogenase in the offspring and enabled them to increment the catalase activity when challenged with MC, whereas 1day of exposure of the parental generation did not. Offspring from non-exposed and 1-day-exposed mothers suffered decreased survival when exposed to MC compared with offspring from 7-day-exposed mothers; survival was correlated with the elevated activity of GST, malate dehydrogenase and catalase, suggesting maternal transfer of activation factors. However, increased survival occurred at the expense of individual growth. These results suggest that transgenerational effects are provoked by MC in D. magna, which may explain the observed acquirement of enhanced tolerance over generations.