The common carp, Cyprinus carpio, is a stenohaline species but can tolerate some changes in environmental salinity. This study aimed to better understand their osmoregulatory response to salinity increases. Messenger RNA expression of the Na⁺K⁺ ATPase α3 (NKAα3) and Aquaporin 3α (AQP3α) genes and histomorphological changes of the chloride cells were investigated on common carp gills, as an osmoregulatory organ in experimental and control groups. The salinity of the experimental group gradually increased to 10 ppt by 3 ppt NaCl per day. The experiment continued for 14 days. Gill samples were preserved in RNA later for RT-qPCR analysis. For histomorphological changes, gill tissue was fixed in glutaraldehyde and processed for electron microscopic examination. RT-qPCR analysis further confirmed that mRNA expression levels of NKAα3 and AQP3α were significantly up-regulated with increasing concentration of NaCl. The tissue-specific NKAα3 and AQP3α transcript response in the gill suggests a critical role of NKAα3 and AQP3α expression in fish for successful acclimation to increased salinity. Also, chloride cells demonstrated hypertrophy with an increased number and size of mitochondria. The current findings clarified that increasing salinity modulates NKAα3 and AQP3α genes expression in common carp, and the gill chloride cells manifest profound histomorphological alteration these findings are critical for the future application to cultivate the common carp in water with high salinity, especially in countries suffering from scarce freshwater.