Due to their many practical applications, engineered cerium dioxide (CeO2) nanoparticles (NPs) are commonly used today, although there are justified concerns about the environmental risks of their usage. Studies to date have shown that CeO2 NPs do not pose a lethal hazard to hydrobiocenoses at environmentally relevant concentrations, but that they induce significant negative sublethal effects. Therefore, intensive work is being done on the adaptation of standard ecotoxicological tests with the development of new, sublethal biomarkers. The present study aims to examine the sublethal effects of prolonged exposure to CeO2 NPs (2.5; 25; 250 and 2500 mg of CeO2 NPs per 1 kg of sediment) on the morphological features of the non-biting aquatic midge Chironomus riparius. Morphological variation was examined by means of two approaches: (1) Deformity rate analysis (analysis of visible morphological malformations) and (2) Geometric morphometric analysis (analysis of differences in the size and shape of the larval mandibles and mentums, as well as adult male and female wings). Changes in all the morphological structures examined were observed using a geometric morphometric approach at low and very high concentrations of CeO2 NPs (2.5 and 2500 mg of CeO2 NPs per 1 kg of sediment). The potential reduction of sexual dimorphism resulting from downsizing of the wings in females was observed. These results indicate that the sublethal changes observed in chironomids exposed to CeO2 NPs are significant and may potentially lead to further changes in metabolism, diet and behavior, which may lead to repercussions of as yet unexamined proportions. Considering our findings, and the advantages of geometric morphometrics (precision, uniformity, accurate qualification, quantification, and visualization of fine morphological changes), this approach is proven to be an exceptional assessment tool, with great applicative potential in the ecotoxicological testing of nanoparticles.