Anthropogenic activities such as the use of pesticides may affect aquatic biota populations, due to potential agricultural runoffs or disposals. Carbendazim is one example of a widely used fungicide with a high potential to end up in aquatic ecosystems through runoff. Deleterious effects observed at the individual level are possibly explained by changes in homeostasis at the cellular level, and both factors can then be used to predict effects at the population level. In the present study, an isoclonal population of Daphnia magna (clone K6) was exposed to a concentration that mimics relevant levels of carbendazim in the environment over 12 generations. The effects of carbendazim were assessed in some generations using the following endpoints: biochemical biomarkers (cholinesterase, catalase, and glutathione-S-transferase), lipid peroxidation and energy-related parameters (carbohydrates, lipids, and proteins along with available energy and energy consumption), parental longevity, and population growth (r). Long-term exposure to carbendazim had no effect on the intrinsic rate of natural increase (r) of adult D. magna, but longevity was decreased at the F12 generation compared to that of control. Differences between the exposed and nonexposed populations were found for cholinesterase, glutathione-S-transferase, and lipid peroxidation. However, for catalase and energy-related parameters, no differences were observed between these 2 populations. Natural variability was seen throughout the test period, under control conditions, within the 12 generations. Overall, carbendazim induced some effects at the subcellular level that translated into changes in longevity but these later vanished in terms of population effects. Environ Toxicol Chem 2019;38:412-422. C 2018 SETAC