ABSTRACT A comprehensive field investigation was conducted on 300 specimens of common carp ( Cyprinus carpio ) from the Godavari Basin in Nanded and Parbhani districts between May 2024 and April 2025. The protozoan parasite Chilodonella uncinata was identified in 65 fish, resulting in a prevalence rate of 21.1%. Accurate identification was achieved using morphometric analysis under light microscopy, silver nitrate staining, and scanning electron microscopy (SEM), which revealed detailed ciliary structures confirming the species. Histopathological examination of infected gill and skin tissues showed marked pathological changes, including epithelial hyperplasia, lamellar fusion, and infiltration of inflammatory cells, indicating a potential impact on respiratory efficiency and general fish health. This represents the first confirmed report of C. uncinata infecting C. carpio in this region. The findings emphasize the necessity of routine parasite screening and targeted management strategies in aquaculture. Additionally, the study demonstrated that environmental factors, such as elevated water temperature, increased turbidity, reduced dissolved oxygen, and nutrient enrichment, significantly influence the prevalence of the parasite. These results underscore the importance of integrating environmental monitoring into fish health programs to mitigate the spread of protozoan infections and to support sustainable aquaculture development in freshwater ecosystems.