Much of the recent literature concerning the threat posed by anthropogenic microscopic pollution has focussed on marine organisms although freshwater environments face the same degree of pollution and therefore risk. Although several studies have documented the ingestion of nanoparticles (NPs) in species of the pelagic freshwater rotifer genus Brachionus, unambiguous evidence for its cellular uptake in this group remains lacking. We therefore used transmission electron microscopy (TEM) of ultrathin sections through the digestive tract of individuals of Brachionus calyciflorus exposed in vitro to citrate stabilized gold nanoparticles (AuCit NPs) in their culture medium to provide the first concrete evidence for the cellular uptake of NPs in rotifers, a group of organisms that comprise an important part of the zooplankton community. Using this method, AuCit NPs with average diameters of 8.5 ± 1.4 nm and 12.5 ± 1.5 nm could be localized clearly within large vacuoles within the stomach cells. Moreover, the occasional presence of pits containing AuCit NPs in the outer membranes of these cells hints that the particles are taken up by some form of endocytosis. In all cases, the ingestion of AuCit NPs showed lethal effects after only one day with virtually no individuals surviving more than two days of exposure. Combined with the TEM evidence above, we hypothesize that death might derive from some form of lysosomal overload. In total, our results document the potential threat that microscopic pollution also poses for freshwater organisms. Through this, we hope that additional emphasis in this context will be directed toward freshwater environments and the potential for such pollution both to enter as well as to move up the food chain via trophic transfer events.