Three‐spined sticklebacks (Gasterosteus aculeatus L.) of the Camargue region (Rhone delta, northern Mediterranean Sea) occupy coastal mesohaline lagoons and freshwater canals. In this study, the acclimation capacity to different salinities of a population living in freshwater canals was investigated. Freshwater (FW; 5 ‰) individuals were compared to fish acclimated for at least 2 weeks to brackish water (BW; 15 ‰) and seawater (SW; 30 ‰). Blood osmotic pressure and gill Na+/K+‐ATPase (NKA) gene expression of the α1 subunit and α1a and α1b isoforms were determined at these salinities. NKA protein expression in the gill ionocytes and the remodelling of these cells were also investigated through NKA immunolabelling and electron microscopy. Blood osmolalities of fish acclimated to FW, BW and SW were significantly different. Branchial NKA α1a and α1b expressions also differed, with a higher expression of NKA α1b in fish acclimated to SW. Gill ionocytes in fish acclimated to FW were located along the lamellae and at their base and appeared elongated, whereas these cells were restricted to gill filaments in fish acclimated to SW with a round shape. Finally, electron microscopy revealed three different types of apical structures for these ionocytes: a honeycomb‐like structure and a dome shape in FW, and deeply encrypted in SW. This study shows that ionocyte cell type and morphology, and gill NKA expression are salinity‐dependent. This branchial remodelling is directly linked to the physiological homeostatic status reached by the fish. It also highlights that sticklebacks of the Camargue region can rapidly acclimate to different salinities and can easily migrate between FW canals and mesohaline coastal lagoons.