Despite their ecological importance and ability to react to environmental changes, including pollution, monogonont rotifers have never been used in palaeolimnological studies because they do not leave subfossil remains. In this study, we tested the possibility of using rotifer resting eggs as a proxy for reconstruction of changes in biodiversity during chronic copper pollution and recovery of a deep sudalpine lake (Lake Orta, Italy). The lake was selected owing to a rich history of previous studies that explored species-specific responses to environmental stressors. Rotifer-based results were compared with those on ephippia and on previously investigated Cladocera subfossil remains. Responses of Rotifera resting eggs to environmental changes were clear and consistent with those previously observed on Cladocera. The abundance of resting eggs increased during pollution, and new morphotypes appeared in addition to those already present. However, overall diversity decreased sharply, as a few morphotypes became dominant. Resting eggs of Brachionus calyciflorus as old as ca. 100 years were still fully viable; viability was not affected by toxic conditions of the environment in which the eggs were produced. Over a period of ca. 80 years, all resting eggs of B. calyciflorus belonged to a single clone, the most widely distributed one in North America. Cladocera ephippia started to accumulate later and at a lower level of abundance than rotifer resting eggs. Overall, Cladocera ephippia were, however, less effective than rotifers in tracing lake historical changes. The results point out at the great potential of using rotifer resting eggs in palaeolimnological reconstructions.