Microcystins that are cell-bound within Microcystis have demonstrated the ability to cause lethal and reproductive impairment in Daphnia , who constitute an important part of aquatic food chains and are known to feed on viable cyanobacterial cells. Recent advances in environmental toxicogenomics can be used to better understand the mechanistic effects from exposure to cell-bound microcystins in Daphnia ; however, there remains a need to examine the effects of microcystins exposure as a function of dose and time in order to help elucidate the progression of (sub-)lethal effects. This study examines the effects of cell-bound microcystin exposure in Daphnia magna as a function of dose and time with shotgun proteomics in order to measure and provide insightful evidence describing functional mechanisms from, and relationships between, protein populations in response to toxic Microcystis aeruginosa. We further characterize the life-history fitness of D. magna in the presence of toxic exposure by measuring somatic growth rate. Chronic dietary exposure to cell-bound microcystins reduced the somatic growth rate of D. magna. Through proteomics analysis, we identified a significant increase in abundance of proteins related to reproductive success and development, removal of superoxide radicals, and motor activity in D. magna parents exposed to cell-bound microcystins at sub-lethal concentrations. We also identified a significant decrease in abundance of proteins related to apoptosis, metabolism, DNA damage repair, and immunity in D. magna neonates. This information will improve our understanding of the risks posed by cell-bound microcystins to cladocerans in freshwater ecosystems. Unlabelled Image • Proteome measurements reveal sub-lethal effects caused by cell-bound microcystins in Daphnia. • Decrease in somatic growth rate from exposure to cell-bound microcystins • Increase in proteins related to fertilization, defense, and motor activity for parents • Decrease in proteins related to apoptosis, DNA repair, and immunity for neonates [ABSTRACT FROM AUTHOR]