Laboratory ecotoxicity tests and biomonitoring in aquatic systems are currently based on the active component of invertebrate communities. Even though dormant egg banks are crucial for the long term survival and community dynamics of many aquatic organisms, the effects of anthropogenic activities on dormant egg bank dynamics have rarely been studied. In this study we investigated the effects of two pesticides with a different mode of action (carbaryl and fenoxycarb) on hatching of Daphnia magna dormant eggs (ephippia) as well as on survival, growth and reproduction of the hatched neonates. Dormant eggs were exposed to the pesticides simultaneously to incubation under conditions that induce hatching (long daylight and 20 °C). Carbaryl had no negative effects on embryonic development or hatching rate up to concentrations almost 1,000 times the median effect concentration (EC50) of neonate survival in acute tests. Fenoxycarb, however, had a significant dose-related effect by delaying or completely stopping the hatching process and caused severe abnormalities in developing individuals. Both pesticides had significant negative effects on survival and reproduction of the hatchlings. These results indicate that, in addition to inducing mortality of active individuals, pesticides can affect zooplankton communities by altering hatching dynamics and life history traits of hatched individuals. We briefly discuss how such pollution induced changes in the benthic-pelagic coupling could translate into trans-generational effects impacting ecological and evolutionary dynamics.