As all arthropods, microcrustaceans shed their chitinous exoskeleton (cuticule, peritrophic membrane) to develop and grow. While the molting is the most crucial stage in their life cycle, it remains poorly investigated in term of pollutant biodistribution within the organisms. In this paper, we used optical, electronic, and X ray-based microscopies to study the uptake and release of CeO2 nanoparticles by/from Daphnia pulex over a molting stage. We measured that D. pulex molts every 59 ± 21 h (confidence interval) with growth rates about 1.1 or 1.8 μm per stage as a function of the pieces measured. Ingestion via food chain was the main route of CeO2 nanoparticles uptake by D. pulex. The presence of algae during the exposure to nanoparticles (sub-lethal doses) enhanced by a factor of 3 the dry weight concentration of Ce on the whole D. pulex. Nanoparticles were localized in the gut content, in direct contact with the peritrophic membrane, and on the cuticle. Interestingly, the depuration (24 h with Chlorella pseudomonas) was not efficient to remove the nanoparticles from the organisms. From 40% to 100% (depending on the feeding regime during exposure) of the CeO2 taken up by D. pulex is not release after the depuration process. However, we demonstrated for the first time that the shedding of the chitinous exoskeleton was the crucial mechanism governing the released of CeO2 nanoparticles regardless of the feeding regime during exposure.